Identification and characterization of a bacterial hydrosulphide ion channel

Nature

Volumn 483, Issue 7390, 2012, Pages 494-497

  Czyzewski, Bryan K ^a   Wang, Da Neng ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FORMIC ACID; HYDROSULPHIDE ION CHANNEL; ION CHANNEL; NITRITE; PROTEOLIPOSOME; UNCLASSIFIED DRUG;

BACTERIUM; CRYSTAL STRUCTURE; DETOXIFICATION; ENZYME ACTIVITY; HYDROGEN SULFIDE; ION; MEMBRANE; METABOLITE; ORIGIN OF LIFE; PATHOGEN; PHYSIOLOGY; REGENERATION; SULFATE; SULFITE; TOXIC MATERIAL;

ARTICLE; BACTERIUM IDENTIFICATION; BINDING AFFINITY; CLOSTRIDIUM DIFFICILE; CRYSTAL STRUCTURE; GENETIC ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE;

BACTERIAL PROTEINS; CLOSTRIDIUM DIFFICILE; CRYSTALLOGRAPHY, X-RAY; FORMIC ACIDS; ION CHANNEL GATING; ION CHANNELS; ION TRANSPORT; MODELS, BIOLOGICAL; MODELS, MOLECULAR; NITRITES; OPERON; PROTEOLIPIDS; PROTON-MOTIVE FORCE; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; SULFIDES;

BACTERIA (MICROORGANISMS); CLOSTRIDIUM; CLOSTRIDIUM DIFFICILE; SALMONELLA;

EID: 84862803226     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature10881     Document Type: Article

References (43)

1. Wähtershäser, G. Groundworks for an evolutionary biochemistry: the ironsulphur world. Prog. Biophys. Mol. Biol. 58, 85-201 (1992).
2. Kabil, O.&Banerjee, R. Redox biochemistry of hydrogen sulfide. J. Biol. Chem. 285, 21903-21907 (2010).
3. Dhillon, A., Goswami, S., Riley, M., Teske, A. & Sogin, M. Domain evolution and functional diversification of sulfite reductases. Astrobiology 5, 18-29 (2005). (Pubitemid 40345651)
4. Rabus, R., Hansen, T. & Widdel, F. in The Prokaryotes: Ecophysiology and Biochemistry Vol. 2 (eds Dworkin, M. et al.) 659-768 (Springer, 2006).
5. 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 HS2, rather than H2S. J. Exp. Biol. 200, 2609-2616 (1997). (Pubitemid 27477019)
6. Jacques, A. G. The kinetics of penetration: XII. Hydrogen sulfide. J. Gen. Physiol. 19, 397-418 (1936).
7. 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). (Pubitemid 33051376)
8. Lee, J. K. et al. Structural basis for conductance by the archaeal aquaporinAqpMat 1.68A? . Proc. Natl Acad. Sci. USA 102, 18932-18937 (2005). (Pubitemid 43049544)
9. Mathai, J. C. et al. No facilitator required for membrane transport of hydrogen sulfide. Proc. Natl Acad. Sci. USA 106, 16633-16638 (2009).
10. Suppmann, B. & Sawers, G. Isolation and characterization of hypophosphite-resistantmutants of Escherichia coli: identification of the FocA protein, encoded by the pfl operon, as a putative formate transporter. Mol. Microbiol. 11, 965-982 (1994). (Pubitemid 24199664)
11. Waight, A. B., Love, J. & Wang, D. N. Structure and mechanism of a pentameric formate channel. Nature Struct. Mol. Biol. 17, 31-37 (2010).
12. 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).
13. 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).
14. Hirshfield, I. N., Terzulli, S.&O'Byrne, C.Weak organic acids: a panoply of effectson bacteria. Sci. Prog. 86, 245-269 (2003).
15. Wang, Y. et al. Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel. Nature 462, 467-472 (2009).
16. Lu, W. et al. pH-dependent gating in a FocA formate channel. Science 332, 352-354 (2011).
17. 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).
18. Crane, B. R.&Getzoff, E. D. The relationship between structure and function for the sulfite reductases. Curr. Opin. Struct. Biol. 6, 744-756 (1996). (Pubitemid 27007658)
19. Hallenbeck, P. C., Clark, M. A. & Barrett, E. L. Characterization of anaerobic sulfite reductionby Salmonella typhimuriumand purificationof the anaerobically induced sulfite reductase. J. Bacteriol. 171, 3008-3015 (1989). (Pubitemid 19145646)
20. 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).
21. Doyle, D. A. et al. The structure of the potassium channel: molecular basis of K1 conduction and selectivity. Science 280, 69-77 (1998). (Pubitemid 28169082)
22. 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). (Pubitemid 24373233)
23. 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).
24. 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).
25. Tai, C. H. et al.Characterization of the allosteric anion-binding site of O-acetylserine sulfhydrylase. Biochemistry 40, 7446-7452 (2001).
26. Hille, B. Ionic Channels of Excitable Membranes 362-389 (Sinauer, 1992).
27. Yasui, M. et al. Rapid gating and anion permeability of an intracellular aquaporin. Nature 402, 184-187 (1999).
28. Rychkov, G. Y., Pusch, M., Roberts, M. L., Jentsch, T. J. & Bretag, A. H. Permeation and block of the skeletalmuscle chloride channel, ClC-1, by foreign anions. J. Gen. Physiol. 111, 653-665 (1998). (Pubitemid 28232188)
29. Simons, J. & Jordan, K. D. Ab initio electronic structure of anions. Chem. Rev. 87, 535-555 (1987).
30. Penel, S. et al. Databases of homologous gene families for comparative genomics. BMC Bioinformatics 10 (suppl. 6), S3 (2009).
31. Clamp, M., Cuff, J., Searle, S. M. & Barton, G. J. The Jalview Java alignment editor. Bioinformatics 20, 426-427 (2004). (Pubitemid 38262778)
32. Han, M. V. & Zmasek, C. M. phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10, 356 (2009).
33. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Sayers, E. W. GenBank. Nucleic Acids Res. 39, D32-D37 (2011).
34. Auer, M. et al. High-yield expression and functional analysis of Escherichia coli glycerol-3-phosphate transporter. Biochemistry 40, 6628-6635 (2001). (Pubitemid 32552786)
35. Wang, D. N. et al. Practical aspects of overexpressing bacterial secondary membrane transporters for structural studies. Biochim. Biophys. Acta1610,23-36 (2003).
36. Cadene, M. & Chait, B. A robust, detergent friendly method for mass spectrometry analysis of integral membrane proteins. Anal. Chem. 72, 5655-5658 (2000).
37. Li, X. D. et al. Monomeric state and ligand binding of recombinant GABA transporter from Escherichia coli. FEBS Lett. 494, 165-169 (2001).
38. Safferling, M. et al. The TetL tetracycline efflux protein from Bacillus subtilis is a dimer in themembraneand in detergent solution. Biochemistry42,13969-13976 (2003). (Pubitemid 37466622)
39. Otwinowski, Z. & Miror, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276A, 307-326 (1997). (Pubitemid 27085611)
40. Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948-1954 (2002). (Pubitemid 35337293)
41. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004). (Pubitemid 41742764)
42. 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). (Pubitemid 27302826)
43. DeLano, W. L. The PyMOL Molecular Graphics System Æhttp://www. pymol.orgæ (2002).