Acknowledgements The U.S. Environmental Protection Agency, through its Office of Research and Development and the RARE program, funded, managed, and collaborated in the research described herein. This work has been subjected to the agency’s administrative review and has been approved for external publication. Any opinions expressed in this paper are those of the authors and do not necessarily reflect the views of the agency; therefore, no official endorsement should be inferred. Any mention of trade names or commercial products does not constitute endorsement or recommendation

for use. The authors thank B. Iker, M. Kyrias, D. Strattan, B. Farrell, E. Luber, M. Nolan, C. Salvatori, J. Shelton, and P. Bermudez for their assistance in the laboratory and the field. H. Ryu received funding through a fellowship from the National Research Council. This work was also supported in part through funding from QNZ datasheet the Department of Energy grant DE-FG02-02ER15317, a Director’s Postdoctoral Fellowship from Argonne National Laboratory to T. Flynn, and the SBR SFA at Argonne National Laboratory which is supported by the Subsurface Biogeochemical

Research Program, Office of Biological and Environmental Compound C datasheet Research, Office of Science, U.S. Department of Energy (DOE), under contract DE-AC02-06CH11357. Electronic supplementary material Additional file 1: Table S1: Energy available for microbial respiration. Figure S1. Collectors

curves showing how the total richness of the bacterial community increases with greater sampling depth. Figure S2. Collectors curves showing how the total richness of the archaeal community increases PRKACG with greater sampling depth. Figure S3. Available energy (∆G A) for either the anaerobic oxidation of methane (AOM) or methanogenesis with increasing amounts of dihydrogen (H2) in Mahomet aquifer groundwater. Figure S4. Multidimensional scaling (MDS) LY2606368 ordination of the Bray-Curtis coefficients of similarity for attached microbial communities in the Mahomet aquifer. Figure S5. Multidimensional scaling (MDS) ordination of the Bray-Curtis coefficients of similarity for suspended microbial communities in the Mahomet aquifer. (DOCX 460 KB) References 1. Fredrickson JK, Balkwill DL: Geomicrobial processes and biodiversity in the deep terrestrial subsurface. Geomicrobiol J 2006, 23:345–356.CrossRef 2. Bethke CM, Ding D, Jin Q, Sanford RA: Origin of microbiological zoning in groundwater flows. Geology 2008, 36:739–742.CrossRef 3. Park J, Sanford RA, Bethke CM: Microbial activity and chemical weathering in the Middendorf aquifer, South Carolina. Chem Geol 2009, 258:232–241.CrossRef 4. Borch T, Kretzschmar R, Kappler A, Cappellen PV, Ginder-Vogel M, Voegelin A, Campbell K: Biogeochemical redox processes and their impact on contaminant dynamics. Environ Sci Technol 2009, 44:15–23.CrossRef 5.

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They are

essentially involved in regulation or sensing. In the family of VFT-containing sensor-kinases of which BvgS is a prototype, PAS domains are frequently found between the transmembrane segment and the kinase domain. Sequences of the bvgAS locus from a number of B. pertussis, Bordetella bronchiseptica and Bordetella parapertussis isolates have shown the remarkable conservation of the PAS domain in BvgS, supporting the idea that it is functionally important [19]. In this work, we identified specific amino acid residues in the PAS domain whose substitutions abolish BvgS activity. They map to three different locations: at the interfaces between the PAS core and its flanking N-terminal and C-terminal α helices, selleck kinase inhibitor and in the PAS cavity. These results support a key transmission function for the PAS domain in BvgS, related to its selleck chemical critical

position between the periplasmic and kinase domains. The PAS domain in BvgS needs to be tightly folded to fulfill this role, because significantly loosening the PAS core or its connections with upstream and downstream helices dramatically affects BvgS activity. We found that the PASBvg domain dimerises in E. coli, and we propose that it does so in full-length BvgS as well. Dimer formation is consistent with earlier findings that the kinase domain of BvgS dimerises [39–41]. The increased solubility of recombinant PASBvg proteins containing large portions of the C- and N-terminal flanking α helices argues that the latter contribute to dimer formation, as described for some other PAS domains [42, 43]. The outer surfaces of the β sheet of PAS cores are generally hydrophobic, and in other PAS dimers they participate in the interface or are apposed to flanking helices [8, 13, 44]. This also appears Amisulpride to be the case for PASBvg. The

structural model is also in good agreement with proposed mechanisms of signal transmission by other PAS domains, with the β sheet participating in signaling [43, 45, 46]. In the PASBvg model the β sheet is well positioned to relay information to the flanking C-terminal α helix and thus to the kinase domain. In the current mechanistic model, BvgS is active in its basal state, and this activity requires the integrity of the periplasmic domain, since specific substitutions or insertions in the periplasmic region of BvgS abolish activity [6, 47]. We thus propose that in its basal, non-liganded state the periplasmic domain adopts a conformation that provides a NVP-HSP990 clinical trial positive signal to the system. The binding of nicotinate to the VFT2 domain modifies this conformation and strongly decreases the positive-signaling capability of the protein [6]. The distinct conformational states of the periplasmic domain most likely impose distinct conformations onto the membrane segment that are propagated via long α helices to the PASBvg domain and from there to the kinase domain underneath.