Abstract
The hydrosulphide ion (HS−) and its undissociated form, hydrogen sulphide (H2S), which are believed to have been critical to the origin of life on Earth1, remain important in physiology and cellular signalling2. As a major metabolite in anaerobic bacterial growth, hydrogen sulphide is a product of both assimilatory and dissimilatory sulphate reduction2,3,4. These pathways can reduce various oxidized sulphur compounds including sulphate, sulphite and thiosulphate. The dissimilatory sulphate reduction pathway uses this molecule as the terminal electron acceptor for anaerobic respiration, in which process it produces excess amounts of H2S (ref. 4). The reduction of sulphite is a key intermediate step in all sulphate reduction pathways. In Clostridium and Salmonella, an inducible sulphite reductase is directly linked to the regeneration of NAD+, which has been suggested to have a role in energy production and growth, as well as in the detoxification of sulphite3. Above a certain concentration threshold, both H2S and HS− inhibit cell growth by binding the metal centres of enzymes and cytochrome oxidase5, necessitating a release mechanism for the export of this toxic metabolite from the cell5,6,7,8,9. Here we report the identification of a hydrosulphide ion channel in the pathogen Clostridium difficile through a combination of genetic, biochemical and functional approaches. The HS− channel is a member of the formate/nitrite transport family, in which about 50 hydrosulphide ion channels form a third subfamily alongside those for formate10,11 (FocA) and for nitrite12 (NirC). The hydrosulphide ion channel is permeable to formate and nitrite as well as to HS− ions. Such polyspecificity can be explained by the conserved ion selectivity filter observed in the channel’s crystal structure. The channel has a low open probability and is tightly regulated, to avoid decoupling of the membrane proton gradient.
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Protein Data Bank
Data deposits
The atomic coordinates and structure factors of HSC for high, medium and low pH have been deposited in the Protein Data Bank under accession codes 3TDO, 3TDR and 3TDP, respectively, and those of the Lys 16 Ser, Leu 82 Val, Thr 84 Ala, Lys 148 Glu and Phe 194 Ile mutants have been deposited under the codes 3TE2, 3TDX, 3TE1, 3TE0 and 3TDS, respectively.
References
Wächtershäuser, G. Groundworks for an evolutionary biochemistry: the iron-sulphur world. Prog. Biophys. Mol. Biol. 58, 85–201 (1992)
Kabil, O. & Banerjee, R. Redox biochemistry of hydrogen sulfide. J. Biol. Chem. 285, 21903–21907 (2010)
Dhillon, A., Goswami, S., Riley, M., Teske, A. & Sogin, M. Domain evolution and functional diversification of sulfite reductases. Astrobiology 5, 18–29 (2005)
Rabus, R., Hansen, T. & Widdel, F. in The Prokaryotes: Ecophysiology and Biochemistry Vol. 2 (eds Dworkin, M., et al.) 659–768 (Springer, 2006)
Goffredi, S. K., Childress, J. J., Desaulniers, N. T. & Lallier, F. J. Sulfide acquisition by the vent worm Riftia pachyptila appears to be via uptake of HS−, rather than H2S. J. Exp. Biol. 200, 2609–2616 (1997)
Jacques, A. G. The kinetics of penetration: XII. Hydrogen sulfide. J. Gen. Physiol. 19, 397–418 (1936)
Freytag, J. K. et al. A paradox resolved: sulfide acquisition by roots of seep tubeworms sustains net chemoautotrophy. Proc. Natl Acad. Sci. USA 98, 13408–13413 (2001)
Lee, J. K. et al. Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 Å. Proc. Natl Acad. Sci. USA 102, 18932–18937 (2005)
Mathai, J. C. et al. No facilitator required for membrane transport of hydrogen sulfide. Proc. Natl Acad. Sci. USA 106, 16633–16638 (2009)
Suppmann, B. & Sawers, G. Isolation and characterization of hypophosphite–resistant mutants of Escherichia coli: identification of the FocA protein, encoded by the pfl operon, as a putative formate transporter. Mol. Microbiol. 11, 965–982 (1994)
Waight, A. B., Love, J. & Wang, D. N. Structure and mechanism of a pentameric formate channel. Nature Struct. Mol. Biol. 17, 31–37 (2010)
Jia, W., Tovell, N., Clegg, S., Trimmer, M. & Cole, J. A single channel for nitrate uptake, nitrite export and nitrite uptake by Escherichia coli NarU and a role for NirC in nitrite export and uptake. Biochem. J. 417, 297–304 (2009)
Hughes, M. N., Centelles, M. N. & Moore, K. P. Making and working with hydrogen sulfide: the chemistry and generation of hydrogen sulfide in vitro and its measurement in vivo: a review. Free Radic. Biol. Med. 47, 1346–1353 (2009)
Hirshfield, I. N., Terzulli, S. & O’Byrne, C. Weak organic acids: a panoply of effects on bacteria. Sci. Prog. 86, 245–269 (2003)
Wang, Y. et al. Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel. Nature 462, 467–472 (2009)
Lu, W. et al. pH-dependent gating in a FocA formate channel. Science 332, 352–354 (2011)
Das, P., Lahiri, A. & Chakravortty, D. Novel role of the nitrite transporter NirC in Salmonella pathogenesis: SPI2-dependent suppression of inducible nitric oxide synthase in activated macrophages. Microbiology 155, 2476–2489 (2009)
Crane, B. R. & Getzoff, E. D. The relationship between structure and function for the sulfite reductases. Curr. Opin. Struct. Biol. 6, 744–756 (1996)
Hallenbeck, P. C., Clark, M. A. & Barrett, E. L. Characterization of anaerobic sulfite reduction by Salmonella typhimurium and purification of the anaerobically induced sulfite reductase. J. Bacteriol. 171, 3008–3015 (1989)
Wilson, W. J. &. Blair, E. M. M.’v. A combination of bismuth and sodium sulphite affording an enrichment and selective medium for the typhoid-paratyphoid groups of bacteria. J. Pathol. Bacteriol. 29, 310–311 (1926)
Doyle, D. A. et al. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280, 69–77 (1998)
Middleton, R. E., Pheasant, D. J. & Miller, C. Purification, reconstitution, and subunit composition of a voltage-gated chloride channel from Torpedo electroplax. Biochemistry 33, 13189–13198 (1994)
Savage, D. F., O’Connell, J. D., III, Miercke, L. J., Finer–Moore, J. & Stroud, R. M. Structural context shapes the aquaporin selectivity filter. Proc. Natl Acad. Sci. USA 107, 17164–17169 (2010)
Feth, S., Gibbs, G. V., Boisen, M. B., Jr & Myers, R. H. Promolecule radii for nitrides, oxides, and sulfides. A comparison with effective ionic and crystal radii. J. Phys. Chem. 97, 11445–11450 (1993)
Tai, C. H. et al. Characterization of the allosteric anion-binding site of O-acetylserine sulfhydrylase. Biochemistry 40, 7446–7452 (2001)
Hille, B. Ionic Channels of Excitable Membranes 362–389 (Sinauer, 1992)
Yasui, M. et al. Rapid gating and anion permeability of an intracellular aquaporin. Nature 402, 184–187 (1999)
Rychkov, G. Y., Pusch, M., Roberts, M. L., Jentsch, T. J. & Bretag, A. H. Permeation and block of the skeletal muscle chloride channel, ClC-1, by foreign anions. J. Gen. Physiol. 111, 653–665 (1998)
Simons, J. & Jordan, K. D. Ab initio electronic structure of anions. Chem. Rev. 87, 535–555 (1987)
Penel, S. et al. Databases of homologous gene families for comparative genomics. BMC Bioinformatics 10 (suppl. 6). S3 (2009)
Clamp, M., Cuff, J., Searle, S. M. & Barton, G. J. The Jalview Java alignment editor. Bioinformatics 20, 426–427 (2004)
Han, M. V. & Zmasek, C. M. phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10, 356 (2009)
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Sayers, E. W. GenBank. Nucleic Acids Res. 39, D32–D37 (2011)
Auer, M. et al. High-yield expression and functional analysis of Escherichia coli glycerol-3-phosphate transporter. Biochemistry 40, 6628–6635 (2001)
Wang, D. N. et al. Practical aspects of overexpressing bacterial secondary membrane transporters for structural studies. Biochim. Biophys. Acta 1610, 23–36 (2003)
Cadene, M. & Chait, B. A robust, detergent friendly method for mass spectrometry analysis of integral membrane proteins. Anal. Chem. 72, 5655–5658 (2000)
Li, X. D. et al. Monomeric state and ligand binding of recombinant GABA transporter from Escherichia coli. FEBS Lett. 494, 165–169 (2001)
Safferling, M. et al. The TetL tetracycline efflux protein from Bacillus subtilis is a dimer in the membrane and in detergent solution. Biochemistry 42, 13969–13976 (2003)
Otwinowski, Z. & Miror, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276A, 307–326 (1997)
Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002)
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)
Smart, O. S., Neduvelil, J. G., Wang, X., Wallace, B. A. & Sansom, M. S. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14, 354–360,–376 (1996)
DeLano, W. L., The PyMOL Molecular Graphics System 〈http://www.pymol.org〉 (2002)
Acknowledgements
We are grateful the staff at beamlines X25 and X29 of the National Synchrotron Light Source at Brookhaven National Laboratory and at beamline 23ID of the Advanced Photon Source at Argonne National Laboratory for assistance in X-ray diffraction experiments. We thank A. B. Waight for suggesting the project; J. J. Marden for assistance with cloning of mutants; T. Neubert and S. Blais for mass spectrometry measurements; the 2010 CCP4 Workshop for assistance in processing diffraction data; and A. David, H. Jackson, N. K. Karpowich, J. J. Marden, R. L. Mancusso, Y. Pan and M. Zhou for discussions. This work was financially supported by the NIH (R01-GM093825, R01-DK073973, R01-MH083840 and U54-GM075026). B.K.C. was partly supported by an NIH Supplement Grant to Promote Diversity in Health-Related Research (R01-DK053973-08A1S1) and an NIH pre-doctoral fellowship (F31-AI086072).
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B.K.C. did the experiments. B.K.C. and D.-N.W. wrote the manuscript.
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Czyzewski, B., Wang, DN. Identification and characterization of a bacterial hydrosulphide ion channel. Nature 483, 494–497 (2012). https://doi.org/10.1038/nature10881
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DOI: https://doi.org/10.1038/nature10881
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