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Histidine kinase

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https://www.readbyqxmd.com/read/29457883/mapping-the-h-nox-hk-binding-interface-in-vibrio-cholerae-by-hydrogen-deuterium-exchange-mass-spectrometry
#1
Yirui Guo, Anthony T Iavarone, Matthew M Cooper, Michael A Marletta
Heme-nitric oxide/oxygen binding (H-NOX) proteins are a group of hemoproteins that bind diatomic gas ligands such as nitric oxide (NO) and oxygen (O2 ). H-NOX proteins typically regulate histidine kinases (HK) located within the same operon. It has been reported that NO-bound H-NOXs inhibit cognate histidine kinase autophosphorylation in bacterial H-NOX/HK complexes, however, a detailed mechanism of NO-mediated regulation of the H-NOX/HK activity remains unknown. In this study, the binding interface of Vibrio cholerae (Vc) H-NOX/HK complex was characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) and further validated by mutagenesis, leading to a new model for NO-dependent kinase inhibition...
February 19, 2018: Biochemistry
https://www.readbyqxmd.com/read/29453948/noncritical-signaling-role-of-a-kinase-receptor-interaction-surface-in-the-escherichia-coli-chemosensory-core-complex
#2
Germán E Piñas, Michael D DeSantis, John S Parkinson
In E. coli chemosensory arrays, transmembrane receptors, a histidine autokinase CheA, and a scaffolding protein CheW interact to form an extended hexagonal lattice of signaling complexes. One interaction, previously assigned a crucial signaling role, occurs between chemoreceptors and the CheW-binding P5 domain of CheA. Structural studies showed a receptor helix fitting into a hydrophobic cleft at the boundary between P5 subdomains. Our work aimed to elucidate the in vivo roles of the receptor-P5 interface, employing as a model the interaction between E...
February 14, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29451272/the-ndpk-nme-superfamily-state-of-the-art
#3
EDITORIAL
Mathieu Boissan, Uwe Schlattner, Marie-Lise Lacombe
Nucleoside diphosphate kinases (NDPK) are nucleotide metabolism enzymes encoded by NME genes (also called NM23). Given the fact that not all NME-encoded proteins are catalytically active NDPKs and that NM23 generally refers to clinical studies on metastasis, we use here NME/NDPK to denote the proteins. Since their discovery in the 1950's, NMEs/NDPKs have been shown to be involved in multiple physiological and pathological cellular processes, but the molecular mechanisms have not been fully determined. Recent progress in elucidating these underlying mechanisms has been presented by experts in the field at the 10th International Congress on the NDPK/NME/AWD protein family in October 2016 in Dubrovnik, Croatia, and is summarized in review articles or original research in this and an upcoming issue of Laboratory Investigation...
February 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29429584/differential-daptomycin-resistance-development-in-staphyloccocus-aureus-strains-with-active-and-mutated-gra-regulatory-systems
#4
Anna Müller, Fabian Grein, Andreas Otto, Kathrin Gries, Dmitriy Orlov, Vladimir Zarubaev, Myriam Girard, Xinwei Sher, Olga Shamova, Terry Roemer, Patrice François, Dörte Becher, Tanja Schneider, Hans-Georg Sahl
The first-in-class lipopeptide antibiotic daptomycin (DAP) is highly active against Gram-positive pathogens including ß-lactam and glycopeptide resistant strains. Its molecular mode of action remains enigmatic, since a defined target has not been identified so far and multiple effects, primarily on the cell envelope have been observed. Reduced DAP susceptibility has been described in S. aureus and enterococci after prolonged treatment courses. In line with its pleiotropic antibiotic activities, a unique, defined molecular mechanism of resistance has not emerged, instead non-susceptibility appears often accompanied by alterations in membrane composition and changes in cell wall homeostasis...
December 21, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/29429090/tuning-chemoreceptor-signaling-by-positioning-aromatic-residues-at-the-lipid-aqueous-interface
#5
Rahmi Yusuf, Robert J Lawrence, Lucy V Eke, Roger R Draheim
Aromatic tuning facilitates stimulus-independent modulation of receptor output. The methodology is based upon the affinity of amphipathic aromatic residues, namely Trp and Tyr, for the polar-hydrophobic interfaces found within biological membranes. Here, we describe the application of aromatic tuning within the aspartate chemoreceptor of Escherichia coli (Tar). We have also employed the method within other related proteins, such as sensor histidine kinases (SHKs), and therefore hope that other research groups find it useful to modulate signal output from their receptor of interest...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29429088/monitoring-two-component-sensor-kinases-with-a-chemotaxis-signal-readout
#6
Run-Zhi Lai, John S Parkinson
Bacteria use two-component signal transduction systems to elicit adaptive responses to environmental changes. The simplest of these systems comprises a transmembrane sensor with histidine kinase activity and its cytoplasmic response regulator partner. Stimulus-response studies of two-component signaling systems typically employ expression reporters, such as β-galactosidase, that operate with relatively slow kinetics and low precision. In this chapter, we illustrate a new strategy for directly measuring the signaling activities of two-component sensor kinases in vivo...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29429087/fret-analysis-of-the-chemotaxis-pathway-response
#7
Anja Paulick, Victor Sourjik
Most motile bacteria follow spatial gradients of chemical and physical stimuli in their environment. In Escherichia coli and other bacteria, the best characterized chemotaxis is in gradients of amino acids or sugars, but other physiological stimuli such as pH, osmolarity, redox potentials, and temperature are also known to elicit tactic responses. These multiple environmental stimuli are integrated and processed within a highly sophisticated chemotaxis network to generate coordinated chemotaxis behavior, which features high sensitivity, a wide dynamic range, and robustness against variations in background stimulation, protein levels, and temperature...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29429086/in-vitro-assay-for-measuring-receptor-kinase-activity-in-the-bacillus-subtilis-chemotaxis-pathway
#8
Hanna E Walukiewicz, George W Ordal, Christopher V Rao
The sensing apparatus of the Bacillus subtilis chemotaxis pathway involves a complex consisting of chemoreceptors, the CheA histidine kinase, and the CheV and CheW adaptor proteins. Attractants and repellents alter the rate of CheA autophosphorylation, either by directly binding the receptors or by indirectly interacting with them through intermediate binding proteins. We describe an in vitro assay for measuring receptor-kinase activity in B. subtilis. This assay has been used to investigate the mechanism of signal transduction in B...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29424663/a-large-scale-mutational-analysis-of-two-component-signaling-systems-of-lonsdalea-quercina-revealed-that-kdpd-kdpe-regulates-bacterial-virulence-against-host-poplar-trees
#9
Ruo-Lan Yang, Chao-Ying Deng, Jin-Wei Wei, Wei He, Ai-Ning Li, Wei Qian
Poplar, which is a dominant species in plant communities distributed in the northern hemisphere, is commonly used as a model plant in forestry studies. Poplar production can be inhibited by infections caused by bacteria, including Lonsdalea quercina subsp. populi, which is a Gram-negative bacterium responsible for bark canker disease. However, the molecular basis of the pathogenesis remains uncharacterized. In this study, we annotated the two-component signal transduction systems (TCSs) encoded by the L. quercina subsp...
February 9, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29422490/dibutyl-phthalate-alters-the-metabolic-pathways-of-microbes-in-black-soils
#10
Weihui Xu, Yimin You, Zhigang Wang, Wenjing Chen, Jin Zeng, Xiaosong Zhao, Yunpeng Su
Dibutyl phthalate (DBP) is well known as a high-priority pollutant. This study explored the impacts of DBP on the metabolic pathways of microbes in black soils in the short term (20 days). The results showed that the microbial communities were changed in black soils with DBP. In nitrogen cycling, the abundances of the genes were elevated by DBP. DBP contamination facilitated 3'-phosphoadenosine-5'-phosphosulfate (PAPS) formation, and the gene flux of sulfate metabolism was increased. The total abundances of ABC transporters and the gene abundances of the monosaccharide-transporting ATPases MalK and MsmK were increased by DBP...
February 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29420866/a-miniaturized-e-coli-green-light-sensor-with-high-dynamic-range
#11
Nicholas Ting Xun Ong, Jeffrey J Tabor
Genetically-engineered photoreceptors enable unrivaled control over gene expression. Previously, we ported the Synechocystis PCC 6803 CcaSR two-component system, which is activated by green light and de-activated by red, into E. coli, resulting in a sensor with 6-fold dynamic range. Later, we optimized pathway protein expression levels and the output promoter sequence to decrease transcriptional leakiness and increase the dynamic range to approximately 120-fold. These CcaSR v1.0 and 2.0 systems have been used for precise quantitative, temporal, and spatial control of gene expression for a variety of applications...
February 8, 2018: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29399821/study-of-the-affinity-between-the-protein-kinase-pka-and-homoarginine-containing-peptides-derived-from-kemptide-free-energy-perturbation-fep-calculations
#12
Karel Mena-Ulecia, Fabian Gonzalez-Norambuena, Ariela Vergara-Jaque, Horacio Poblete, William Tiznado, Julio Caballero
Protein kinases (PKs) discriminate between closely related sequences that contain serine, threonine, and/or tyrosine residues. Such specificity is defined by the amino acid sequence surrounding the phosphorylatable residue, so that it is possible to identify an optimal recognition motif (ORM) for each PK. The ORM for the protein kinase A (PKA), a well-known member of the PK family, is the sequence RRX(S/T)X, where arginines at the -3 and -2 positions play a key role with respect to the primed phosphorylation site...
February 5, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29358334/the-qseg-lipoprotein-impacts-the-virulence-of-enterohemorrhagic-e-coli-and-citrobacter-rodentium-and-regulates-flagellar-phase-variation-in-salmonella-enterica-serovar-typhimurium
#13
Elizabeth A Cameron, Charley C Gruber, Jennifer M Ritchie, Matthew K Waldor, Vanessa Sperandio
The QseEF histidine kinase/response regulator system modulates expression of enterohemorrhagic E. coli (EHEC) and Salmonella enterica serovar Typhimurium (Stm) virulence genes in response to the host neurotransmitters epinephrine and norepinephrine. QseG, which encodes an outer membrane lipoprotein, is co-transcribed with qseEF in these enteric pathogens, but there is little knowledge of its role in virulence. Here, we found that in EHEC QseG interacts with the type three secretion system (T3SS) gate protein SepL, and modulates the kinetics of attaching and effacing (AE) lesion formation on tissue-cultured cells...
January 22, 2018: Infection and Immunity
https://www.readbyqxmd.com/read/29352085/the-expression-of-bacteriocin-production-and-self-resistance-in-lactobacillus-brevis-174a-is-mediated-by-two-regulatory-proteins
#14
Masafumi Noda, Rumi Miyauchi, Narandalai Danshiitsoodol, Yasuyuki Matoba, Takanori Kumagai, Masanori Sugiyama
We have previously shown that a lactic acid bacterium Lactobacillus (Lb.) brevis 174A isolated from a Citrus iyo fruit produces bacteriocin designated brevicin 174A, which is comprised of two antibacterial polypeptides (designated brevicin 174A-β and 174A-γ). We have also found a gene cluster, composed of eight open reading frames (ORFs), that contains genes for the biosynthesis of brevicin 174A, self-resistance to its own bacteriocin, and two transcriptional regulatory proteins.Some lactic acid bacterial strains have a system to start the production of bacteriocin at an adequate stage of the growth...
January 19, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29323112/signaling-ammonium-across-membranes-through-an-ammonium-sensor-histidine-kinase
#15
Tobias Pflüger, Camila F Hernández, Philipp Lewe, Fabian Frank, Haydyn Mertens, Dmitri Svergun, Manfred W Baumstark, Vladimir Y Lunin, Mike S M Jetten, Susana L A Andrade
Sensing and uptake of external ammonium is essential for anaerobic ammonium-oxidizing (anammox) bacteria, and is typically the domain of the ubiquitous Amt/Rh ammonium transporters. Here, we report on the structure and function of an ammonium sensor/transducer from the anammox bacterium "Candidatus Kuenenia stuttgartiensis" that combines a membrane-integral ammonium transporter domain with a fused histidine kinase. It contains a high-affinity ammonium binding site not present in assimilatory Amt proteins. The levels of phosphorylated histidine in the kinase are coupled to the presence of ammonium, as conformational changes during signal recognition by the Amt module are transduced internally to modulate the kinase activity...
January 11, 2018: Nature Communications
https://www.readbyqxmd.com/read/29314743/sensor-kinase-kinb-and-its-pathway-associated-key-factors-sense-the-signal-of-nutrition-starvation-in-sporulation-of-bacillus%C3%A2-subtilis
#16
Weipeng Liu, Zeying He, Feng Gao, Jinyuan Yan, Xiaowei Huang
Bacillus subtilis responds to environmental stress cues and develops endospores for survival. In the process of endospore formation, sporulation initiation is a vital stage and this stage is governed by autophosphorylation of the sensor histidine kinases. The second major sensor kinase KinB perceives the intracellular changes of GTP and ATP during sporulation. However, determination of the environmental signals as well as its related signaling pathway of KinB requires further elucidation. Our current study found that, contrary to the sporulation failure induced by ΔkinA in the nutrient-rich 2× SG medium, the sensor kinase KinB sensed the environmental cues in the nutrient-poor MM medium...
January 3, 2018: MicrobiologyOpen
https://www.readbyqxmd.com/read/29306353/vibrio-cholerae-genomic-diversity-within-and-between-patients
#17
Inès Levade, Yves Terrat, Jean-Baptiste Leducq, Ana A Weil, Leslie M Mayo-Smith, Fahima Chowdhury, Ashraful I Khan, Jacques Boncy, Josiane Buteau, Louise C Ivers, Edward T Ryan, Richelle C Charles, Stephen B Calderwood, Firdausi Qadri, Jason B Harris, Regina C LaRocque, B Jesse Shapiro
Cholera is a severe, water-borne diarrhoeal disease caused by toxin-producing strains of the bacterium Vibrio cholerae. Comparative genomics has revealed 'waves' of cholera transmission and evolution, in which clones are successively replaced over decades and centuries. However, the extent of V. cholerae genetic diversity within an epidemic or even within an individual patient is poorly understood. Here, we characterized V. cholerae genomic diversity at a micro-epidemiological level within and between individual patients from Bangladesh and Haiti...
December 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29299752/backbone-resonance-assignment-of-the-response-regulator-protein-phobnf20d-from-escherichia-coli
#18
Xinhui Kou, Xinghong Liu, Yixiang Liu, Conggang Li, Maili Liu, Ling Jiang
PhoB is a response regulator of the PhoR/PhoB two-component signal transduction system that is involved in the regulation of the phosphate (Pho) regulon of Escherichia coli. PhoB has two domains, receiver domain and effector domain. The receiver domain can be phosphorylated by its cognate histidine kinase PhoR and the phosphorylation induces conformational changes of the full length protein of PhoB that promote the DNA binding and transcription. Three-dimensional crystal structures of PhoB receiver domain (PhoBN) have been solved under apo or BeF3- (a phosphoryl analog) binding forms and it has been found that PhoBN is dimerized in both situations...
January 3, 2018: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29290041/oligomeric-states-in-sodium-ion-dependent-regulation-of-cyanobacterial-histidine-kinase-2
#19
Iskander M Ibrahim, Liang Wang, Sujith Puthiyaveetil, Norbert Krauß, Jon Nield, John F Allen
Two-component signal transduction systems (TCSs) consist of sensor histidine kinases and response regulators. TCSs mediate adaptation to environmental changes in bacteria, plants, fungi and protists. Histidine kinase 2 (Hik2) is a sensor histidine kinase found in all known cyanobacteria and as chloroplast sensor kinase in eukaryotic algae and plants. Sodium ions have been shown to inhibit the autophosphorylation activity of Hik2 with precedes phosphoryl transfer to response regulators, but the mechanism of inhibition has not been determined...
December 30, 2017: Protoplasma
https://www.readbyqxmd.com/read/29285524/analysis-of-the-genes-involved-in-thiocyanate-oxidation-during-growth-in-continuous-culture-of-the-haloalkaliphilic-sulfur-oxidizing-bacterium-thioalkalivibrio-thiocyanoxidans-arh-2t-using-transcriptomics
#20
Tom Berben, Cherel Balkema, Dimitry Y Sorokin, Gerard Muyzer
Thiocyanate (N=C-S-) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and the cyanate pathway, of which only the former has been fully characterized. Use of the cyanate pathway has been shown in only 10 strains of Thioalkalivibrio, a genus of obligately haloalkaliphilic sulfur-oxidizing Gammaproteobacteria found in soda lakes...
November 2017: MSystems
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