Abstract
Motile bacteria and archaea respond to chemical and physical stimuli seeking optimal conditions for survival. To this end transmembrane chemo- and photoreceptors organized in large arrays initiate signaling cascades and ultimately regulate the rotation of flagellar motors. To unravel the molecular mechanism of signaling in an archaeal phototaxis complex we performed coarse-grained molecular dynamics simulations of a trimer of receptor/transducer dimers, namely NpSRII/NpHtrII from Natronomonas pharaonis. Signaling is regulated by a reversible methylation mechanism called adaptation, which also influences the level of basal receptor activation. Mimicking two extreme methylation states in our simulations we found conformational changes for the transmembrane region of NpSRII/NpHtrII which resemble experimentally observed light-induced changes. Further downstream in the cytoplasmic domain of the transducer the signal propagates via distinct changes in the dynamics of HAMP1, HAMP2, the adaptation domain and the binding region for the kinase CheA, where conformational rearrangements were found to be subtle. Overall these observations suggest a signaling mechanism based on dynamic allostery resembling models previously proposed for E. coli chemoreceptors, indicating similar properties of signal transduction for archaeal photoreceptors and bacterial chemoreceptors.
Highlights
Phototaxis in archaea is mediated by integral membrane protein complexes consisting of bacteriorhodopsin-like receptors, sensory rhodopsins, and tightly bound transmembrane signal transducers, Htrs
Comparing fully methylated and demethylated complexes reveals an interconversion between states of different dynamics along the coiled-coil bundle, which might represent the essential characteristics of the signal transfer from the membrane to the binding sites of the downstream kinase CheA
To reveal structural and dynamical effects of methylation/demethylation of the NpSRII/ NpHtrII complex we have built a coarse-grained model of trimer-of-dimers based on a preequilibrated all-atom model of the 2:2 NpSRII/NpHtrII complex
Summary
Phototaxis in archaea is mediated by integral membrane protein complexes consisting of bacteriorhodopsin-like receptors, sensory rhodopsins, and tightly bound transmembrane signal transducers, Htrs. The archaeal genomes comprise homologs of the principal elements of bacterial two-component systems: the histidine kinase CheA, the response regulators CheY and CheB, and the methyltransferase CheR [2] This homology suggests that the core properties of signal propagation are conserved and similar in archaeal phototaxis and bacterial chemotaxis [3]. The phototaxis system of Natronomonas pharaonis, which is composed of sensory rhodopsin II, NpSRII, in a 2:2 complex with its cognate transducer, NpHtrII, and the Che proteins mentioned above, allows these archaea to avoid harmful blue-green light It represents one of the best-studied archaeal sensor systems [6] that modulates the cell’s swimming behavior by means of a typical two-component cascade (Fig 1). Light induced conformational changes have been observed for NpSRII doi:10.1371/journal.pcbi.1004561.g001
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