Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity

Abstract

Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.

Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review

“…The second example of using SMALPs for SAXS studies of membrane proteins was presented by Nazarenko et al [ 160 ] (see Figure 4 A,B). In this example, the combination of SAXS with size-exclusion chromatography (SEC) was used for structural characterization of the full-length nitrate/nitrite sensor histidine kinase NarQ [ 161 ] from Escherichia coli extracted from native E. coli membrane with SMA polymer. As in the previous example [ 124 ], SAXS curves do not demonstrate the maxima of scattering intensity at q ≈ 0.1–0.2 Å −1 .…”

The Metabolic Adaptation in Response to Nitrate Is Critical for Actinobacillus pleuropneumoniae Growth and Pathogenicity under the Regulation of NarQ/P

“…7). As a ubiquitous cellular process in bacteria, nitrate metabolism involves multiple nitrate sensors, regulators, and enzymes (1,54). E. coli and Salmonella Typhimurium possess two nitrate sensing TCSs, three nitrate reductases, two nitrate transporters, and two nitrite reductases (7,12,54).…”

“…As a ubiquitous cellular process in bacteria, nitrate metabolism involves multiple nitrate sensors, regulators, and enzymes (1,54). E. coli and Salmonella Typhimurium possess two nitrate sensing TCSs, three nitrate reductases, two nitrate transporters, and two nitrite reductases (7,12,54). P. aeruginosa has two nitrate sensors (the NarX sensor kinase homologous to that in E. coli and the McpN chemoreceptor), three nitrate reductases, and the enzymes constituting a complete denitrification pathway (13,55).…”

“…2 , sometimes together with other metabolites (54). In the case of low NO 3 2 concentrations, NarP is induced, enabling periplasmic reductase Nap expression, at which time the extracellular nitrate reduction pathway is active (56,57).…”

Diversity in Sensing and Signaling of Bacterial Sensor Histidine Kinases

“…The main function of HAMP is assumed to be in converting signals from the TM helices to those that can be recognized by the downstream cytoplasmic domains. This conversion can be diagonal scissoring, helical rotation, and transitions between stable and dynamic states [13,[115][116][117][118]. The activity of the catalytic domain is modified by the binding of accessory proteins and second messengers.…”