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.
Highlights
We focus on bacterial nitrate- and nitrite-sensing histidine kinases (HKs) (NSHKs), which are among the best studied two-component systems (TCS)
Based on the gene ordering (Figure 3) and architecture of the nitrate sensors (Figure 5), we suggest that NSHKs may be grouped into three classes: (i) shorter diverging Bacteroidetes sensors; (ii) NarQ-like proteins from Enterobacterales, Pasteurellales, Vibrionales, and Alteromonadales, clustering close to E. coli narQ; and (iii) NarX-like proteins: all other NSHKs
GAFs usually consist of a five- or six-stranded antiparallel β-sheet and four or five αhelices, and they dimerize in such a way that the N-terminal and C-terminal α-helices form parallel coiled coils that are structurally congruent with other HK and TCS modules
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Chemoreceptors and sensory rhodopsin-based photoreceptors are involved in chemo- and phototaxis, but they can perform other functions [10,11,27,28] They form higher-order assemblies composed of trimers-of-dimers of the receptor proteins in complex with the histidine kinase CheA and accessory proteins [27,29]; the activity of CheA is regulated by the receptors [30]. HKs have highly variable modular architectures that, in the minimal form, include the sensor domain, dimerization and histidine phosphotransferase (DHp) domain, and catalytic (CA) domain They can contain a transmembrane (TM) domain and additional signal transduction domains [34] such as HAMP (domain found in histidine kinases, adenylyl cyclases, methyl-accepting proteins, and phosphatases [35,36,37]), PAS (Per-ARNT-Sim [38,39]), and GAF (found in cGMP-specific and stimulated phosphodiesterases, adenylate cyclases, and FhlA [40]), which may or may not be sensors themselves. We review the function of NSHKs, analyze their natural diversity, and describe the available structural information
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