Signaling ammonium across membranes through an ammonium sensor histidine kinase

Abstract

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. The structural analysis of this ammonium sensor by X-ray crystallography and small-angle X-ray-scattering reveals a flexible, bipartite system that recruits a large uptake transporter as a sensory module and modulates its functionality to achieve a mechanistic coupling to a kinase domain in order to trigger downstream signaling events.

Comparative genomics in “Candidatus Kuenenia stuttgartiensis” reveal high genomic plasticity in the overall genome structure, CRISPR loci and surface proteins

“…Abundances of unique peptides belonging to KsCSTR_46980 indicated that KsCSTR_46980 was highly expressed (Table S10), agreeing with the previous finding [11]. A nitrite transporter KsCSTR_14610 (kuste3055, KSMBR1_1070) (0.019%, 441) (abundance, abundance rank; same for further data given below) and an ammonium transporter KsCSTR_43840 (kustc1009, KSMBR1_2627) (0.0039%, 790) were expressed, while the previously characterized ammonium sensor KsCSTR_21800 (kuste3690, KSMBR1_3866) [30] was not found in the proteome.…”

Nutrient Limitation Causes Differential Expression of Transport- and Metabolism Genes in the Compartmentalized Anammox Bacterium Kuenenia stuttgartiensis

“…The two ammonium transporters with histidine kinase domains, amtb_ 1 (KSMBR1_3722) and amtb_ 2 (KSMBR1_3866), were expressed at a low level (<100 RPKM) and expression did not differ between the tested conditions ( Figure 1D ). The amtb 2 gene product (named KsAmt-5 by the authors) has been shown to function as an ammonium sensor in vivo , but does not transport ammonium across the membrane ( Pfluger et al, 2018 ). In fungal species, multiple Mep-type ammonium transporters are present as well and some of these ammonium “transceptors” have a signaling function ( van den Berg et al, 2019 ).…”

“…In summary, we have shown differential gene expression for several of the ammonium and nitrite transporter homologs in K. stuttgartiensis cells and this may partly explain the high copy number of these transporter genes in the genome. It is also clear that at least one of the ammonium transporters has a different function as an ammonium sensor rather than transporter ( Pfluger et al, 2018 ). In addition, it is possible that specific transporters are located in different membranes in the cell.…”

Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument

“…The technique has since resulted in prominent publications (e.g. Berthaud et al, 2012;Meisburger et al, 2016;Pflü ger et al, 2018) and is employed by an increasing number of synchrotron users. The availability of synchrotron beamtime is, though, limited, despite great efforts from beamline administrators to adapt to user needs, and is strictly confined to the scheduled time.…”