Reply to Airola et al.: Linker or a HAMP?

Abstract

This is a response to a letter by Airola et al. (1) We have identified five HAMP domains in DhNik1 by a standard SMART search (2). The boundaries of the HAMP domains selected by us for functional analysis are also in accord with the comprehensive analysis of HAMP domains recently reported by Dunin-Horkawicz and Lupas (3). It appears that the HAMP domains identified by us belong to a group of divergent HAMP domains (most likely F6) as classified by Dunin-Horkawicz and Lupas (3). Although these domains belong to a divergent group, they have distinguishing features, e.g. hydrophobic residues with heptad periodicity, G-(DN)-(LF)-x3-(IVL) motif, and conserved Glu at the beginning of the AS2 helix (4). These features are common in biochemically characterized HAMP domains, which clearly indicate that the domains identified by us are functionally relevant HAMP domains. Therefore, our functional analysis by deleting these domains either serially or one at a time is valid. In their letter, Airola et al. (1) propose that DhNik1 contains four additional divergent HAMP domains. These domains are essentially composed of the linker region (2, 5) with additional overlapping residues from the neighboring HAMP domains. The linker region is highly conserved among group III hybrid histidine kinases (HHKs); however, their role in the functionality of DhNik1 is not clear. The new analysis may therefore help to design mutational analysis of this region. HAMP domains in DhNik1 (group III HHK in general) function as both a sensor and an element for transducing signal to the downstream kinase domain. In this respect, they are quite different from other HAMP domains that transmit input from sensor to the downstream elements only (4, 6). More biochemical and structural studies are required to understand group III HHKs and in this regard the analysis proposed by Airola et al. (1) is an interesting development.