High Throughput Autophosphorylation Assay for Bacterial Protein Histidine Kinases

1997 ◽  
Vol 2 (2) ◽  
pp. 85-90 ◽  
Author(s):  
Siddhartha Roychoudhury ◽  
Susan M. Collins ◽  
Barbara A. Hynd ◽  
Christian N. Parker
Keyword(s):  
High Throughput ◽  
Bacterial Chemotaxis ◽  
Bacterial Protein ◽  
Reaction Conditions ◽  
Histidine Kinases ◽  
Peptide Substrates ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems ◽  
High Throughput Assay

Protein histidine kinases play a major role in bacteria as sensor components in the so-called "two-component" systems involved in signal transduction. We describe a high throughput assay for these kinases using CheA, the bacterial chemotaxis-regulating kinase from Escherichia coil. The purpose of the assay was to monitor ATP-dependent autophosphorylation of the kinase resulting in the phosphorylation of the conserved histidine residue. Unlike most eukaryotic protein kinases, "two-component" kinases are not known to phosphorylate histones and small peptide substrates. This limits the level of phosphorylation and consequently the signal generated in these assays. We, therefore, established the desirable reaction conditions first using the conventional method involving the radio labeling of CheA by [y-32P]ATP followed by gel electrophoresis-based analysis. Next, we converted the assay to a high throughput format in which CheA, autophosphorylated and radiolabeled with [y-33P]ATP, was trapped in a filter via anionic or hydrophobic interaction using diethyl aminoethyl or nitrocellulose-based 96-well filter plates, respectively. Free [y-33P]ATP was removed by washing the wells with high salt buffers. The dried plates were then analyzed for radioactivity associated with the wells by scintillation counting. Finally, we performed and validated the assay in a partially automated format using nitrocellulose-based filter plates.

scholarly journals Blue Light Regulated Two-Component Systems: Enzymatic and Functional Analyses of Light-Oxygen-Voltage (LOV)-Histidine Kinases and Downstream Response Regulators

Biochemistry ◽  
2013 ◽  
Vol 52 (27) ◽  
pp. 4656-4666 ◽  
Author(s):  
Fernando Correa ◽  
Wen-Huang Ko ◽  
Victor Ocasio ◽  
Roberto A. Bogomolni ◽  
Kevin H. Gardner
Keyword(s):  
Blue Light ◽  
Response Regulators ◽  
Histidine Kinases ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems ◽  
Functional Analyses

scholarly journals Two-Component Systems of S. aureus: Signaling and Sensing Mechanisms

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 34
Author(s):  
Lisa Bleul ◽  
Patrice Francois ◽  
Christiane Wolz
Keyword(s):  
Transcriptional Activation ◽  
Drug Targets ◽  
Bacterial Survival ◽  
Histidine Kinases ◽  
Signal Perception ◽  
Signaling Mechanisms ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems ◽  
Sense And Respond

Staphylococcus aureus encodes 16 two-component systems (TCSs) that enable the bacteria to sense and respond to changing environmental conditions. Considering the function of these TCSs in bacterial survival and their potential role as drug targets, it is important to understand the exact mechanisms underlying signal perception. The differences between the sensing of appropriate signals and the transcriptional activation of the TCS system are often not well described, and the signaling mechanisms are only partially understood. Here, we review present insights into which signals are sensed by histidine kinases in S. aureus to promote appropriate gene expression in response to diverse environmental challenges.

scholarly journals Phosphatase activity of the histidine kinases ensures pathway specificity of the ChrSA and HrrSA two‐component systems in C orynebacterium glutamicum

2014 ◽  
Vol 92 (6) ◽  
pp. 1326-1342 ◽  
Author(s):  
Eva Hentschel ◽  
Christina Mack ◽  
Cornelia Gätgens ◽  
Michael Bott ◽  
Melanie Brocker ◽  
...  
Keyword(s):  
Phosphatase Activity ◽  
Histidine Kinases ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems

scholarly journals Accurate prediction of bacterial two-component signaling with a deep recurrent neural network ORAKLE

2019 ◽  
Author(s):  
Jan Balewski ◽  
Zachary F. Hallberg
Keyword(s):  
Neural Network ◽  
Amino Acid ◽  
Response Regulator ◽  
Amino Acid Sequences ◽  
Histidine Kinases ◽  
Deep Recurrent Neural Network ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems ◽  
Recommender Algorithm

AbstractTwo-component systems (2CS) are a primary method that bacteria use to detect and respond to environmental stimuli. Receptor histidine kinases (HK) detect an environmental signal, activating the appropriate response regulator (RR). Genes for such cognate HK-RR pairs are often located proximally on the chromosome, allowing easier identification of the target for a particular signal. However, almost half of all HK and RR proteins are orphans, with no nearby partner, complicating identification of the proteins that respond to a particular signal. To address this problem, we trained a neural network on the amino acid sequences of known 2CS pairs. Next, we developed a recommender algorithm that ranks a set of HKs for an arbitrary fixed RR and arbitrary species whose amino acid sequences are known. The recommender strongly favors known 2CS pairs, and correctly selects orphan pairs in Escherichia coli. We expect that use of these results will permit rapid discovery of orphan HK-RR pairs.

scholarly journals Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Felipe Trajtenberg ◽  
Juan A Imelio ◽  
Matías R Machado ◽  
Nicole Larrieux ◽  
Marcelo A Marti ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Response Regulators ◽  
Histidine Kinases ◽  
Signaling Systems ◽  
Input Signals ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems ◽  
Conformational Rearrangements ◽  
Phosphoryl Groups

Two-component systems (TCS) are protein machineries that enable cells to respond to input signals. Histidine kinases (HK) are the sensory component, transferring information toward downstream response regulators (RR). HKs transfer phosphoryl groups to their specific RRs, but also dephosphorylate them, overall ensuring proper signaling. The mechanisms by which HKs discriminate between such disparate directions, are yet unknown. We now disclose crystal structures of the HK:RR complex DesK:DesR from Bacillus subtilis, comprising snapshots of the phosphotransfer and the dephosphorylation reactions. The HK dictates the reactional outcome through conformational rearrangements that include the reactive histidine. The phosphotransfer center is asymmetric, poised for dissociative nucleophilic substitution. The structural bases of HK phosphatase/phosphotransferase control are uncovered, and the unexpected discovery of a dissociative reactional center, sheds light on the evolution of TCS phosphotransfer reversibility. Our findings should be applicable to a broad range of signaling systems and instrumental in synthetic TCS rewiring.

scholarly journals What do archaeal and eukaryotic histidine kinases sense?

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 2145 ◽  
Author(s):  
Nicolas Papon ◽  
Ann M. Stock
Keyword(s):  
Response Regulator ◽  
Single Step ◽  
Adaptive Responses ◽  
Histidine Kinases ◽  
Regulatory Processes ◽  
Component Systems ◽  
Two Component ◽  
Broad Array ◽  
Domains Of Life ◽  
Two Component Systems

Signal transduction systems configured around a core phosphotransfer step between a histidine kinase and a cognate response regulator protein occur in organisms from all domains of life. These systems, termed two-component systems, constitute the majority of multi-component signaling pathways in Bacteria but are less prevalent in Archaea and Eukarya. The core signaling domains are modular, allowing versatility in configuration of components into single-step phosphotransfer and multi-step phosphorelay pathways, the former being predominant in bacteria and the latter in eukaryotes. Two-component systems regulate key cellular regulatory processes that provide adaptive responses to environmental stimuli and are of interest for the development of antimicrobial therapeutics, biotechnology applications, and biosensor engineering. In bacteria, two-component systems have been found to mediate responses to an extremely broad array of extracellular and intracellular chemical and physical stimuli, whereas in archaea and eukaryotes, the use of two-component systems is more limited. This review summarizes recent advances in exploring the repertoire of sensor histidine kinases in the Archaea and Eukarya domains of life.

scholarly journals Specificity Residues Determine Binding Affinity for Two-Component Signal Transduction Systems

mBio ◽  
2013 ◽  
Vol 4 (6) ◽  
Author(s):  
Jonathan W. Willett ◽  
Nitija Tiwari ◽  
Susanne Müller ◽  
Katherine R. Hummels ◽  
Jon C. D. Houtman ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Myxococcus Xanthus ◽  
Titration Calorimetry ◽  
Signaling Proteins ◽  
Response Regulators ◽  
Histidine Kinases ◽  
Content Type ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems

ABSTRACTTwo-component systems (TCS) comprise histidine kinases and their cognate response regulators and allow bacteria to sense and respond to a wide variety of signals. Histidine kinases (HKs) phosphorylate and dephosphorylate their cognate response regulators (RRs) in response to stimuli. In general, these reactions appear to be highly specific and require an appropriate association between the HK and RR proteins. TheMyxococcus xanthusgenome encodes one of the largest repertoires of signaling proteins in bacteria (685 open reading frames [ORFs]), including at least 127 HKs and at least 143 RRs. Of these, 27 arebona fideNtrC-family response regulators, 21 of which are encoded adjacent to their predicted cognate kinases. Using system-wide profiling methods, we determined that the HK-NtrC RR pairs display a kinetic preference during both phosphotransfer and phosphatase functions, thereby defining cognate signaling systems inM. xanthus. Isothermal titration calorimetry measurements indicated that cognate HK-RR pairs interact with dissociation constants (Kd) of approximately 1 µM, while noncognate pairs had no measurable binding. Lastly, a chimera generated between the histidine kinase, CrdS, and HK1190 revealed that residues conferring phosphotransfer and phosphatase specificity dictate binding affinity, thereby establishing discrete protein-protein interactions which prevent cross talk. The data indicate that binding affinity is a critical parameter governing system-wide signaling fidelity for bacterial signal transduction proteins.IMPORTANCEUsingin vitrophosphotransfer and phosphatase profiling assays and isothermal titration calorimetry, we have taken a system-wide approach to demonstrate specificity for a family of two-component signaling proteins inMyxococcus xanthus. Our results demonstrate that previously identified specificity residues dictate binding affinity and that phosphatase specificity follows phosphotransfer specificity for cognate HK-RR pairs. The data indicate that preferential binding affinity is the basis for signaling fidelity in bacterial two-component systems.

scholarly journals Unequal twins: Unraveling the reaction mechanism of dimeric histidine kinases

2020 ◽  
Vol 295 (23) ◽  
pp. 8118-8119
Author(s):  
Wolfgang Gärtner
Keyword(s):  
Basic Function ◽  
Response Regulators ◽  
Histidine Kinases ◽  
Open Questions ◽  
Component Systems ◽  
Two Component ◽  
New Strategy ◽  
Two Component Systems ◽  
Future Work ◽  
Partner Proteins

Histidine kinases (HKs), together with their partner proteins, the response regulators (RRs), form the ubiquitous two-component systems that are global players in control and adjustment of microbial lifestyle. Although their basic function (i.e. the transfer of a phosphate group from the HK to its RR partner) is simple to articulate, deciphering the molecular details of this process has proven anything but simple, especially when quantitative aspects come into play. Bouillet et al. report a series of elegant and sophisticated experiments to quantitatively understand HK functions, clearing up several open questions and providing a new strategy for future work in the field.

scholarly journals Specificity of Subtilin-Mediated Activation of Histidine Kinase SpaK

2017 ◽  
Vol 83 (18) ◽  
Author(s):  
Christoph Geiger ◽  
Tobias Spieß ◽  
Sophie Marianne Korn ◽  
Peter Kötter ◽  
Karl-Dieter Entian
Keyword(s):  
Bacillus Subtilis ◽  
Histidine Kinase ◽  
Two Component System ◽  
Histidine Kinases ◽  
Component System ◽  
Content Type ◽  
Component Systems ◽  
Two Component ◽  
Specific Manner ◽  
Two Component Systems

ABSTRACT Autoinduction via two-component systems is a widespread regulatory mechanism that senses environmental and metabolic changes. Although the lantibiotics nisin and subtilin are closely related and share the same lanthionine ring structure, they autoinduce their biosynthesis in a highly specific manner. Subtilin activates only the two-component system SpaRK of Bacillus subtilis, whereas nisin activates solely the two-component system NisRK of Lactococcus lactis. To identify components that determine the specificity of subtilin autoinduction, several variants of the respective lantibiotics were analyzed for their autoinductive capacities. Here, we show that amino acid position 20 is crucial for SpaK activation, as an engineered nisin molecule with phenylalanine at position 20 (nisin N20F) was able to activate SpaK in a specific manner. In combination with the N-terminal tryptophan of subtilin (nisin I1W/N20F), SpaK autoinduction reached almost the level of subtilin-mediated autoinduction. Furthermore, the overall structure of subtilin is also important for its association with the histidine kinase. The destruction of the second lanthionine ring (subtilin C11A, ring B), as well as mutations that interfere with the flexibility of the hinge region located between lanthionine rings C and D (subtilin L21P/Q22P), abolished SpaK autoinduction. Although the C-terminal part of subtilin is needed for efficient SpaK autoinduction, the destruction of lanthionine rings D and E had no measurable impact. Based on these findings, a model for the interaction of subtilin with histidine kinase SpaK was established. IMPORTANCE Although two-component systems are important regulatory systems that sense environmental changes, very little information on the molecular mechanism of sensing or the interaction of the sensor with its respective kinase is available. The strong specificity of linear lantibiotics such as subtilin and nisin for their respective kinases provides an excellent model system to unravel the structural needs of these lantibiotics for activating histidine kinases in a specific manner. More than that, the biosyntheses of lantibiotics are autoinduced via two-component systems. Therefore, an understanding of their interactions with histidine kinases is needed for the biosynthesis of newly engineered peptide antibiotics. Using a Bacillus subtilis-based reporter system, we were able to identify the molecular constraints that are necessary for specific SpaK activation and to provide SpaK specificity to nisin with just two point mutations.

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