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Molecular aspects of bacterial pH sensing and homeostasis

Nature Reviews Microbiology volume 9, pages 330–343 (2011)Cite this article

Subjects

Key Points

  • Bacteria that grow optimally in a pH range of near neutral (neutralophiles) require robust mechanisms for cytoplasmic pH homeostasis in order to survive, and in some cases grow, during exposure to acidic or alkaline conditions that are well outside the pH range tolerated for cytoplasmic pH. Extremely acidophilic bacteria maintain a cytoplasmic pH of ∼6.0 while growing at pH 1.0–3.0 in settings such as mining and geothermal areas or acidic soils, and extremely alkaliphilic bacteria maintain a cytoplasmic pH that is as much as 2.3 units below an external pH range of 9.5–11.0 in settings such as alkaline soda lakes, indigo dye plants and sewage plants.

  • Active mechanisms of pH homeostasis under acid challenge conditions include increased expression and activity of proteins or pathways that result in outward proton pumping or the consumption of cytoplasmic protons. Under alkali challenge conditions, mechanisms of pH homeostasis include active proton accumulation or generation in the cytoplasm. Deployment of these strategies and passive adjuncts to the active strategies, such as alterations in membrane permeability to protons, require major transcriptome changes that are mediated by an intricate network of pH-sensing and signalling capabilities.

  • The Na+/H+ antiporter of Escherichia coli, NhaA, is required for alkaline pH homeostasis in the presence of Na+; in addition to its catalytic capacity to support cytoplasmic proton accumulation at high pH, the antiporter protein possesses a pH sensor domain that results in an increase in antiport by three orders of magnitude as the pH is raised from 6.5 to 8.5. Structural studies of three-dimensional crystals of purified NhaA, combined with computational and experimental analyses, have revealed structural and mechanistic features that account for its physiological efficacy.

  • Periplasmic pH homeostasis is a unique strategy among neutralophiles. It enables Helicobacter pylori to colonize the highly acidic surface of the stomach using urease, an acid-gated urea channel (UreI) and cytoplasmic and periplasmic carbonic anhydrases to maintain a periplasmic pH of ∼6.1. The pH gating of UreI involves hydrogen bonding of periplasmic histidines with periplasmic carboxylates. A pair of two-component pH-signalling systems play critical parts in urease trafficking to the inner membrane, where, together with UreI, the enzyme facilitates urea hydrolysis and direct export of the products (CO2, NH3 and NH4+) to the periplasm.

  • Acidophiles and alkaliphiles that grow optimally at extreme pH values typically have adaptations to key proton-translocating complexes (for example, respiratory and ATP synthase complexes) and to their cell surface layers, as reflected by the high and low average isoelectric points, respectively, of their surface-exposed proteins relative to those of the surface-exposed proteins of neutralophiles. These constitutive adaptations promote optimal function at extreme pH, but reduce the growth capacity at near-neutral pH, as shown for the adaptations of the proton-translocating ATP synthase and highly expressed S-layer protein of alkaliphilic Bacillus pseudofirmus OF4.

  • Much has been learned about individual strategies for bacterial pH homeostasis and the molecules involved, but bacterial pH homeostasis is a cell-wide physiological process that deploys and integrates these strategies differently depending on other environmental factors, such as oxygen availability and salinity. The development of systems-level models will depend on further efforts to gather broad-based quantitative 'omics' information as a function of pH under different conditions, and also on more detailed molecular information about the stoichiometric, kinetic and mechanistic properties of key transporters and enzymes.

Abstract

Diverse mechanisms for pH sensing and cytoplasmic pH homeostasis enable most bacteria to tolerate or grow at external pH values that are outside the cytoplasmic pH range they must maintain for growth. The most extreme cases are exemplified by the extremophiles that inhabit environments with a pH of below 3 or above 11. Here, we describe how recent insights into the structure and function of key molecules and their regulators reveal novel strategies of bacterial pH homeostasis. These insights may help us to target certain pathogens more accurately and to harness the capacities of environmental bacteria more efficiently.

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Figure 1: Examples of adaptations by neutralophilic bacteria to manage acid or alkali challenge.
Figure 2: Functional organization of the Escherichia coli Na+/H+ antiporter (NhaA).
Figure 3: Periplasmic buffering by Helicobacter pylori and its regulation.
Figure 4: The hetero-oligomeric Mrp antiporter and other major pH homeostasis strategies of extremely alkaliphilic Bacillus pseudofirmus OF4.

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References

  1. Casey, J. R., Grinstein, S. & Orlowski, J. Sensors and regulators of intracellular pH. Nature Rev. Mol. Cell Biol. 11, 50–61 (2010).

    Article  CAS  Google Scholar 

  2. Padan, E., Bibi, E., Ito, M. & Krulwich, T. A. Alkaline pH homeostasis in bacteria: new insights. Biochim. Biophys. Acta 1717, 67–88 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Slonczewski, J. L., Fujisawa, M., Dopson, M. & Krulwich, T. A. Cytoplasmic pH measurement and homeostasis in bacteria and archaea. Adv. Microb. Physiol. 55, 1–79 (2009). This review of cytoplasmic pH homeostasis in bacteria and archaea provides an overview of the methods that these organisms use to measure cytoplasmic pH, together with observations made in a diverse group of microorganisms.

    Article  PubMed  CAS  Google Scholar 

  4. Cotter, P. D. & Hill, C. Surviving the acid test: responses of gram-positive bacteria to low pH. Microbiol. Mol. Biol. Rev. 67, 429–453 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Quivey, R. G., Kuhnert, W. L. & Hahn, K. Genetics of acid adaptation in oral streptococci. Crit. Rev. Oral Biol. Med. 12, 301–314 (2001).

    Article  CAS  PubMed  Google Scholar 

  6. Audia, J. P. & Foster, J. W. Acid shock accumulation of sigma S in Salmonella enterica involves increased translation, not regulated degradation. J. Mol. Microbiol. Biotechnol. 5, 17–28 (2003).

    Article  CAS  PubMed  Google Scholar 

  7. Foster, J. W. Escherichia coli acid resistance: tales of an amateur acidophile. Nature Rev. Microbiol. 2, 898–907 (2004). An overview of the acid resistance strategies of E. coli , detailing the importance of metabolic re-modelling strategies (such as use of amino acid decarboxylases) for pH homeostasis.

    Article  CAS  Google Scholar 

  8. Rozen, Y., Dyk, T. K., LaRossa, R. A. & Belkin, S. Seawater activation of Escherichia coli gene promoter elements: dominance of rpoS control. Microb. Ecol. 42, 635–643 (2001).

    Article  CAS  PubMed  Google Scholar 

  9. Ingledew, W. J. in Microbiology of Extreme Environments (ed. Edwards, C.) 33–54 (McGraw-Hill, New York, 1990).

    Google Scholar 

  10. Grant, W. D. in Extremophiles (Life Under Extreme External Conditions) Encyclopedia of Life Support Systems (ed. Gerday, C.) (Eolss Publishers, 2003).

    Google Scholar 

  11. Yumoto, I. in Physiology and Biochemistry of Extremophiles (eds Gerday, C. & Glansdorff, N.) 295–310 (ASM Press, Washington, 2007).

    Book  Google Scholar 

  12. Gilmour, R. et al. Two-dimensional gel electrophoresis analyses of pH-dependent protein expression in facultatively alkaliphilic Bacillus pseudofirmus OF4 lead to characterization of an S-layer protein with a role in alkaliphily. J. Bacteriol. 182, 5969–5981 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Hicks, D. B., Liu, J., Fujisawa, M. & Krulwich, T. A. F1F0-ATP synthases of alkaliphilic bacteria: lessons from their adaptations. Biochim. Biophys. Acta 1797, 1362–1377 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Baker-Austin, C. & Dopson, M. Life in acid: pH homoestasis in acidophiles. Trends Microbiol. 15, 165–171 (2007).

    Article  CAS  PubMed  Google Scholar 

  15. Kobayashi, H., Suzuki, T. & Unemoto, T. Streptococcal cytoplasmic pH is regulated by changes in amount and activity of a proton-translocating ATPase. J. Biol. Chem. 261, 627–630 (1986).

    CAS  PubMed  Google Scholar 

  16. Maurer, L. M., Yohannes, E., Bondurant, S. S., Radmacher, M. & Slonczewski, J. L. pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12. J. Bacteriol. 187, 304–319 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Stancik, L. M. et al. pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli. J. Bacteriol. 184, 4246–4258 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Ikegami, M. et al. Enterococcus hirae vacuolar ATPase is expressed in response to pH as well as sodium. FEBS Lett. 454, 67–70 (1999).

    Article  CAS  PubMed  Google Scholar 

  19. Kakinuma, Y. Inorganic cation transport and energy transduction in Enterococcus hirae and other streptococci. Microbiol. Mol. Biol. Rev. 62, 1021–1045 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Padan, E., Venturi, M., Gerchman, Y. & Dover, N. Na+/H+ antiporters. Biochim. Biophys. Acta 1505, 144–157 (2001).

    Article  CAS  PubMed  Google Scholar 

  21. Mesbah, N., Cook, G. & Wiegel, J. The halophilic alkalithermophile Natranaerobius thermophilus adapts to multiple environmental extremes using a large repertoire of Na+(K+)/H+ antiporters. Mol. Microbiol. 74, 270–281 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Macnab, R. M. & Castle, A. M. A variable stoichiometry model for pH homeostasis in bacteria. Biophys. J. 52, 637–647 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Taglicht, D., Padan, E. & Schuldiner, S. Proton-sodium stoichiometry of NhaA, an electrogenic antiporter from Escherichia coli. J. Biol. Chem. 268, 5382–5387 (1993).

    CAS  PubMed  Google Scholar 

  24. Kakinuma, Y. & Igarashi, K. Isolation and properties of Enterococcus hirae mutants defective in the potassium/proton antiport system. J. Bacteriol. 181, 4103–4105 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Waser, M., Hess-Bienz, D., Davies, K. & Solioz, M. Cloning and disruption of a putative NaH-antiporter gene of Enterococcus hirae. J. Biol. Chem. 267, 5396–5400 (1992).

    CAS  PubMed  Google Scholar 

  26. Noguchi, K., Riggins, D. P., Eldahan, K. C., Kitko, R. D. & Slonczewski, J. L. Hydrogenase-3 contributes to anaerobic acid resistance of Escherichia coli. PLoS ONE 5, e10132 (2010). This study shows that hydrogenase 3-mediated consumption of protons for the production of H 2 supports the survival of E. coli under anaerobic and extremely acidic conditions.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. Sheng, J. & Marquis, R. E. Malolactic fermentation by Streptococcus mutans. FEMS Microbiol. Lett. 272, 196–201 (2007).

    Article  CAS  PubMed  Google Scholar 

  28. Gut, H. et al. Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB. EMBO J. 25, 2643–2651 (2006). This work finds that chloride is an activator of the GadB glutamate decarboxylase of E. coli and further describes elements of pH sensing and the response of this key system.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Blankenhorn, D., Phillips, J. & Slonczewski, J. L. Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis. J. Bacteriol. 181, 2209–2216 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Yohannes, E., Barnhart, D. M. & Slonczewski, J. L. pH-dependent catabolic protein expression during anaerobic growth of Escherichia coli K-12. J. Bacteriol. 186, 192–199 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Ruis, N. & Lorén, J. G. Buffering capacity and membrane H+ conductance of neutrophilic and alkalophilic gram-positive bacteria. Appl. Environ. Microbiol. 64, 1344–1349 (1998).

    Google Scholar 

  32. Tomb, J.-F. et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388, 539–547 (1997).

    Article  CAS  PubMed  Google Scholar 

  33. Chi, A. et al. Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughoutput proteomics analysis. Mol. Cell. Proteomics 6, 2239–2251 (2007).

    Article  CAS  PubMed  Google Scholar 

  34. Kennedy, S. P., Ng, W. V., Salzberg, S. L., Hood, L. & DasSarma, S. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res. 11, 1641–1650 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Knight, C. G., Kassen, R., Hebestreit, H. & Rainey, P. B. Global analysis of predicted proteomes: functional adaptation of physical properties. Proc. Natl Acad. Sci. USA 101, 8390–8395 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Broadbent, J. R., Larsen, R. L., Deibel, V. & Steele, J. L. Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress. J. Bacteriol. 192, 2445–2458 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Hayes, E. T. et al. Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12. BMC Microbiol. 6, 89 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Kim, B. H. et al. The formation of cyclopropane fatty acids in Salmonella enterica serovar Typhimurium. Microbiology 151, 209–218 (2005).

    Article  CAS  PubMed  Google Scholar 

  39. Shabala, L. & Ross, T. Cyclopropane fatty acids improve Escherichia coli survival in acidified minimal media by reducing membrane permeability to H+ and enhanced ability to extrude H+. Res. Microbiol. 159, 458–461 (2008).

    Article  CAS  PubMed  Google Scholar 

  40. Guiliani, N. & Jerez, C. A. Molecular cloning, sequencing, and expression of omp-40, the gene coding for the major outer membrane protein from the acidophilic bacterium Thiobacillus ferrooxidans. Appl. Environ. Microbiol. 66, 2318–2324 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Chao, J., Wang, W., Xiao, S. & Liu, X. Response of Acidithiobacillus ferrooxidans ATCC 23270 gene expression to acid stress. World J. Microbiol. Biotechnol. 24, 2103–2109 (2008).

    Article  CAS  Google Scholar 

  42. Mykytczuk, N. C. S., Trevors, J. T., Ferroni, G. D. & Leduc, L. G. Cytoplasmic membrane fluidity and fatty acid composition of Acidithiobacillus ferrooxidans in response to pH stress. Extremophiles 14, 427–441 (2010).

    Article  CAS  PubMed  Google Scholar 

  43. Aono, R., Ito, M. & Machida, T. Contribution of the cell wall component teichuronopeptide to pH homeostasis and alkaliphily in the alkaliphile Bacillus lentus C-125. J. Bacteriol. 181, 6600–6606 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Cao, M. et al. Defining the Bacillus subtilis σW regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. J. Mol. Biol. 316, 443–457 (2002).

    Article  CAS  PubMed  Google Scholar 

  45. Duarte, V. & Latour, J. M. PerR vs OhrR: selective peroxide sensing in Bacillus subtilis. Mol. Biosyst. 6, 316–323 (2010).

    Article  CAS  PubMed  Google Scholar 

  46. Kitko, R. D., Wilks, J. C., Garduque, G. M. & Slonczewski, J. L. Osmolytes contribute to pH homeostasis of Escherichia coli. PLoS ONE 5, e10078 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Wiegert, T., Homuth, G., Versteeg, S. & Schumann, W. Alkaline shock induces the Bacillus subtilis σW regulon. Mol. Microbiol. 41, 59–71 (2001).

    Article  CAS  PubMed  Google Scholar 

  48. Wilks, J. C. et al. Acid and base stress and transcriptomic responses in Bacillus subtilis. Appl. Environ. Microbiol. 75, 981–990 (2009).

    Article  CAS  PubMed  Google Scholar 

  49. Sayed, A. K. & Foster, J. W. A 750 bp sensory integration region directs global control of the Escherichia coli GadE acid resistance regulator. Mol. Microbiol. 71, 1435–1450 (2009).

    Article  CAS  PubMed  Google Scholar 

  50. Wen, Y., Feng, J., Scott, D. R., Marcus, E. A. & Sachs, G. The HP0165-HP0166 two-component system (ArsRS) regulates acid-induced expression of HP1186 α-carbonic anhydrase in Helicobacter pylori by activating the pH-dependent promoter. J. Bacteriol. 189, 2426–2434 (2007). This investigation identifies the role of the acid-responsive TCS ArsRS in H. pylori in regulating the periplasmic carbonic anhydrase, a protein that is essential for acid acclimation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Wen, Y. et al. Acid-adaptive genes of Helicobacter pylori. Infect. Immun. 71, 5921–5939 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Bordi, C., Theraulaz, L., Mejean, V. & Jourlin-Castelli, C. Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli. Mol. Microbiol. 48, 211–223 (2003). An illustration of a TCS that senses and pre-emptively responds to a metabolic change that will lead to a subsequent alkaline challenge to E. coli growth.

    Article  CAS  PubMed  Google Scholar 

  53. Padan, E. The enlightening encounter between structure and function in the NhaA Na+-H+ antiporter. Trends Biochem. Sci. 33, 435–443 (2008). A review describing the structural and functional insights into the mechanism and pH regulation of NhaA that were gained from the NhaA crystal structure.

    Article  CAS  PubMed  Google Scholar 

  54. West, I. C. & Mitchell, P. Proton/sodium ion antiport in Escherichia coli. Biochem. J. 144, 87–90 (1974).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Padan, E., Kozachkov, L., Herz, K. & Rimon, A. NhaA crystal structure: functional-structural insights. J. Exp. Biol. 212, 1593–1603 (2009).

    Article  CAS  PubMed  Google Scholar 

  56. Padan, E., Maisler, N., Taglicht, D., Karpel, R. & Schuldiner, S. Deletion of ant in Escherichia coli reveals its function in adaptation to high salinity and an alternative Na+/H+ antiporter system(s). J. Biol. Chem. 264, 20297–20302 (1989).

    CAS  PubMed  Google Scholar 

  57. Radchenko, M. V. et al. Potassium/proton antiport system of Escherichia coli. J. Biol. Chem. 281, 19822–19829 (2006).

    Article  CAS  PubMed  Google Scholar 

  58. Lewinson, O., Padan, E. & Bibi, E. Alkalitolerance: a biological function for a multidrug transporter in pH homeostasis. Proc. Natl Acad. Sci. USA 101, 14073–14078 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Brett, C. L., Donowitz, M. & Rao, R. Evolutionary origins of eukaryotic sodium/proton exchangers. Am. J. Physiol. Cell. Physiol. 288, C223–239 (2005).

    Article  CAS  PubMed  Google Scholar 

  60. Schushan, M. et al. Model-guided mutagenesis drives functional studies of human NHA2, implicated in hypertension. J. Mol. Biol. 396, 1181–1196 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Xiang, M., Feng, M., Muend, S. & Rao, R. A human Na+/H+ antiporter sharing evolutionary origins with bacterial NhaA may be a candidate gene for essential hypertension. Proc. Natl Acad. Sci. USA 104, 18677–18681 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Malo, M. E. & Fliegel, L. Physiological role and regulation of the Na+/H+ exchanger. Can. J. Physiol. Pharmacol. 84, 1081–1095 (2006).

    Article  CAS  PubMed  Google Scholar 

  63. Slepkov, E. R., Rainey, J. K., Sykes, B. D. & Fliegel, L. Structural and functional analysis of the Na+/H+ exchanger. Biochem. J. 401, 623–633 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Taglicht, D., Padan, E. & Schuldiner, S. Overproduction and purification of a functional Na+/H+ antiporter coded by nhaA (ant) from Escherichia coli. J. Biol. Chem. 266, 11289–11294 (1991).

    CAS  PubMed  Google Scholar 

  65. Hunte, C. et al. Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH. Nature 435, 1197–1202 (2005). The determination of the crystal structure of the NhaA antiporter from E. coli was a breakthrough for our understanding of the functional organization of this antiporter, its mechanism and its regulation by pH.

    Article  CAS  PubMed  Google Scholar 

  66. Screpanti, E. & Hunte, C. Discontinuous membrane helices in transport proteins and their correlation with function. J. Struct. Biol. 159, 261–267 (2007).

    Article  CAS  PubMed  Google Scholar 

  67. Galili, L., Herz, K., Dym, O. & Padan, E. Unraveling functional and structural interactions between transmembrane domains IV and XI of NhaA Na+/H+ antiporter of Escherichia coli. J. Biol. Chem. 279, 23104–23113 (2004).

    Article  CAS  PubMed  Google Scholar 

  68. Padan, E., Venturi, M., Michel, H. & Hunte, C. Production and characterization of monoclonal antibodies directed against native epitopes of NhaA, the Na+/H+ antiporter of Escherichia coli. FEBS Lett. 441, 53–58 (1998).

    Article  CAS  PubMed  Google Scholar 

  69. Rimon, A., Hunte, C., Michel, H. & Padan, E. Epitope mapping of conformational monoclonal antibodies specific to NhaA Na+/H+ antiporter: structural and functional implications. J. Mol. Biol. 379, 471–481 (2008).

    Article  CAS  PubMed  Google Scholar 

  70. Krishnamurthy, H., Piscitelli, C. L. & Gouaux, E. Unlocking the molecular secrets of sodium-coupled transporters. Nature 459, 347–355 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Boudker, O. & Verdon, G. Structural perspectives on secondary active transporters. Trends Pharmacol. Sci. 31, 418–426 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Efremov, R. G., Bardaran, R. & Sazanov, L. A. The architecture of respiratory complex I. Nature 465, 441–445 (2010).

    Article  CAS  PubMed  Google Scholar 

  73. Hunte, C., Zickermann, V. & Brandt, U. Functional modules and structural basis of conformational coupling in mitochondrial complex I. Science 329, 448–451 (2010).

    Article  CAS  PubMed  Google Scholar 

  74. Ohyama, T., Igarashi, K. & Kobayashi, H. Physiological role of the chaA gene in sodium and calcium circulations at a high pH in Escherichia coli. J. Bacteriol. 176, 4311–4315 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Pinner, E., Kotler, Y., Padan, E. & Schuldiner, S. Physiological role of nhaB, a specific Na+/H+ antiporter in Escherichia coli. J. Biol. Chem. 268, 1729–1734 (1993).

    CAS  PubMed  Google Scholar 

  76. Gerchman, Y. et al. Histidine-226 is part of the pH sensor of NhaA, a Na+/H+ antiporter in Escherichia coli. Proc. Natl Acad. Sci. USA 90, 1212–1216 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Herz, K., Rimon, A., Olkhova, E., Kozachkov, L. & Padan, E. Transmembrane segment II of NhaA Na+/H+ antiporter lines the cation passage, and Asp65 is critical for pH activation of the antiporter. J. Biol. Chem. 285, 2211–2220 (2010). This study uses cysteine scanning and tests of accessibility of the cysteines to permeant and impermeant sulphydryl reagents in order to trace the cation passage through NhaA and to identify residues for pH-dependent activation of the antiporter.

    Article  CAS  PubMed  Google Scholar 

  78. Rimon, A., Gerchman, Y., Kariv, Z. & Padan, E. A point mutation (G338S) and its suppressor mutations affect both the pH response of the NhaA-Na+/H+ antiporter as well as the growth phenotype of Escherichia coli. J. Biol. Chem. 273, 26470–26476 (1998).

    Article  CAS  PubMed  Google Scholar 

  79. Gerchman, Y., Rimon, A. & Padan, E. A pH-dependent conformational change of NhaA Na+/H+ antiporter of Escherichia coli involves loop VIII-IX, plays a role in the pH response of the protein, and is maintained by the pure protein in dodecyl maltoside. J. Biol. Chem. 274, 24617–24624 (1999).

    Article  CAS  PubMed  Google Scholar 

  80. Venturi, M. et al. The monoclonal antibody 1F6 identifies a pH-dependent conformational change in the hydrophilic NH2 terminus of NhaA Na+/H+ antiporter of Escherichia coli. J. Biol. Chem. 275, 4734–4742 (2000).

    Article  CAS  PubMed  Google Scholar 

  81. Appel, M., Hizlan, D., Vinothkumar, K. R., Ziegler, C. & Kuhlbrandt, W. Conformations of NhaA, the Na+/H+ exchanger from Escherichia coli, in the pH-activated and ion-translocating state. J. Mol. Biol. 388, 659–672 (2009).

    Article  CAS  PubMed  Google Scholar 

  82. Guan, L. & Kaback, H. R. Lessons from lactose permease. Annu. Rev. Biophys. Biomol. Struct. 35, 67–91 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Olami, Y., Rimon, A., Gerchman, Y., Rothman, A. & Padan, E. Histidine 225, a residue of the NhaA-Na+/H+ antiporter of Escherichia coli is exposed and faces the cell exterior. J. Biol. Chem. 272, 1761–1768 (1997).

    Article  CAS  PubMed  Google Scholar 

  84. Tzubery, T., Rimon, A. & Padan, E. Mutation E252C increases drastically the K m value for Na+ and causes an alkaline shift of the pH dependence of NhaA Na+/H+ antiporter of Escherichia coli. J. Biol. Chem. 279, 3265–3272 (2004).

    Article  CAS  PubMed  Google Scholar 

  85. Tzubery, T., Rimon, A. & Padan, E. Structure-based functional study reveals multiple roles of transmembrane segment IX and loop VIII–IX in NhaA Na+/H+ antiporter of Escherichia coli at physiological pH. J. Biol. Chem. 283, 15975–15987 (2008). Using cysteine scanning together with impermeant and permeant sulphydryl probes, this study shows the importance of a particular membrane-spanning segment of NhaA in the pH-sensing domain of this antiporter.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Kozachkov, L., Herz, K. & Padan, E. Functional and structural interactions of the transmembrane domain X of NhaA, Na+/H+ antiporter of Escherichia coli, at physiological pH. Biochemistry 46, 2419–2430 (2007).

    Article  CAS  PubMed  Google Scholar 

  87. Olkhova, E., Hunte, C., Screpanti, E., Padan, E. & Michel, H. Multiconformation continuum electrostatics analysis of the NhaA Na+/H+ antiporter of Escherichia coli with functional implications. Proc. Natl Acad. Sci. USA 103, 2629–2634 (2006). Crystal structure-based computation reveals clusters of tightly electrostatically interacting residues in a transmembrane region of NhaA, and shows that these clusters have functional importance in pH regulation of the antiporter.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Olkhova, E., Padan, E. & Michel, H. The influence of protonation states on the dynamics of the NhaA antiporter from Escherichia coli. Biophys. J. 92, 3784–3791 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Wilks, J. C. & Slonczewski, J. L. pH of the cytoplasm and periplasm of Escherichia coli: rapid measurement by green fluorescent protein fluorimetry. J. Bacteriol. 189, 5601–5607 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Bauerfeind, P., Garner, R., Dunn, B. E. & Mobley, H. L. Synthesis and activity of Helicobacter pylori urease and catalase at low pH. Gut 40, 25–30 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Cussac, V., Ferrero, R. L. & Labigne, A. Expression of Helicobacter phylori urease genes in Escherichia coli grown under nitrogen-limiting conditions. J. Bacteriol. 174, 2466–2473 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Bury-Mone, S. et al. Roles of α and β carbonic anhydrases of Helicobacter pylori in the urease-dependent response to acidity and in colonization of the murine gastric mucosa. Infect. Immun. 76, 497–509 (2008). This study identifies roles for a β-carbonic anhydrase, as well as an α-carbonic anhydrase, in the urease-dependent acid response and also in gastric colonization of mice by H. pylori.

    Article  CAS  PubMed  Google Scholar 

  93. Bury-Mone, S., Skoulobris, S., Labigne, A. & De Reuse, H. The Helicobacter pylori UreI protein: role in adaptation to acidity and identification of residues essential for its activity and for acid activation. Mol. Microbiol. 42, 1021–1034 (2001).

    Article  CAS  PubMed  Google Scholar 

  94. Mollenhauer-Redtorschek, M., Hanauer, G., Sachs, G. & Melchers, K. Expression of UreI is required for intragastric transit and colonization of gerbil gastric mucosa by Helicobacter pylori. Res. Microbiol. 153, 659–666 (2002).

    Article  Google Scholar 

  95. Weeks, D. L., Eskandari, S., Scott, D. R. & Sachs, G. A H+-gated urea channel: the link between Helicobacter pylori urease and gastric colonization. Science 287, 482–485 (2000). This is the first paper to identify a proton-gated urea channel in bacteria: the UreI channel, which has a central role in acid acclimation of H. pylori.

    Article  CAS  PubMed  Google Scholar 

  96. Scott, D. R. et al. Expression of the Helicobacter pylori ureI gene is required for acidic pH activation of cytoplasmic urease. Infect. Immun. 68, 470–477 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Weeks, D. & Sachs, G. Sites of pH regulation of the urea channel of Helicobacter pylori. Mol. Microbiol. 40, 1249–1259 (2001).

    Article  CAS  PubMed  Google Scholar 

  98. Scott, D. R. et al. Cytoplasmic histidine kinase (HP0244)-regulated assembly of urease with UreI, a channel for urea and its metabolites, CO2, NH3, and NH4+, is necessary for acid survival of Helicobacter pylori. J. Bacteriol. 192, 94–103 (2010).

    Article  CAS  PubMed  Google Scholar 

  99. Clyne, M., Labigne, A. & Drumm, B. Helicobacter pylori requires an acidic environment to survive in the presence of urea. Infect. Immun. 63, 1669–1673 (1995). This article describes the important observation that H. pylori does not survive in the presence of urea under non-acidic conditions, an observation that led to the unravelling of the downregulation of acid-response elements at high pH.

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Beier, D. & Frank, R. Molecular characterization of two-component systems of Helicobacter pylori. J. Bacteriol. 182, 2068–2076 (2000). An elegant study identifing and characterizing all the TCSs in H. pylori.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Panthel, K., Dietz, P., Haas, R. & Beier, D. Two-component systems of Helicobacter pylori contribute to virulence in a mouse infection model. Infect. Immun. 71, 5381–5385 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Müller, S., Götz, M. & Beier, D. Histidine residue 94 is involved in pH sensing by histidine kinase ArsS of Helicobacter pylori. PLoS ONE 4, e6930 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  103. Pflock, M., Kennard, S., Finsterer, N. & Beier, D. Acid-responsive gene regulation in the human pathogen Helicobacter pylori. J. Biotechnol. 126, 52–60 (2006).

    Article  CAS  PubMed  Google Scholar 

  104. Wen, Y., Feng, J., Scott, D. R., Marcus, E. A. & Sachs, G. The pH-responsive regulon of HP0244 (FlgS), the cytoplasmic histidine kinase of Helicobacter pylori. J. Bacteriol. 191, 449–460 (2009).

    Article  CAS  PubMed  Google Scholar 

  105. Hong, W. et al. Medium pH-dependent redistribution of the urease of Helicobacter pylori. J. Med. Microbiol. 52, 211–216 (2003).

    Article  CAS  PubMed  Google Scholar 

  106. Voland, P. et al. Interactions among the seven Helicobacter pylori proteins encoded by the urease gene cluster. Am. J. Physiol. Gastrointest. Liver Physiol. 284, G96–G106 (2003).

    Article  CAS  PubMed  Google Scholar 

  107. Wen, Y., Feng, J., Scott, D. R., Marcus, E. A. & Sachs, G. A cis-encoded antisense small RNA regulated by the HP0165-HP0166 two component system controls expression of ureB in Helicobacter pylori. J. Bacteriol. 193, 40–51 (2011).

    Article  CAS  PubMed  Google Scholar 

  108. Johnson, D. B. in Physiology and Biochemistry of Extremophiles (eds Gerday, C. & Glansdorff, N.) 257–270 (ASM Press, Washington, 2007).

    Book  Google Scholar 

  109. Ferguson, S. J. & Ingledew, W. J. Energetic problems faced by micro-organisms growing or surviving on parsimonious energy sources and at acidic pH: I. Acidithiobacillus ferrooxidans as a paradigm. Biochim. Biophys. Acta 1777, 1471–1479 (2008). An elegant review of the chemiosmotic profile and adaptations that are required to support growth of an extreme acidophile under the combined constraints of limited energy sources and extreme acidity.

    Article  CAS  PubMed  Google Scholar 

  110. Brasseur, G., Bruscella, P., Bonnefoy, V. & Lemesle-Meunier, D. The bc 1 complex of iron-grown acidophilic chemolithotrophic bacterium Acidithiobacillus ferrooxidans functions in the reverse but not in the forward direction. Is there a second bc 1 complex? Biochim. Biophys. Acta 1555, 37–43 (2002).

    Article  CAS  PubMed  Google Scholar 

  111. Valdes, J. et al. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9, 597 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  112. Wisotzkey, J. D., Jurtshuk, P. Jr, Fox, G. E., Deinhard, G. & Poralla, K. Comparative sequence analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and proposal for creation of a new genus, Alicyclobacillus gen. nov. Int. J. Syst. Bacteriol. 42, 263–269 (1992).

    Article  CAS  PubMed  Google Scholar 

  113. Cox, J. C., Nicholls, D. G. & Ingledew, W. J. Transmembrane electrical potential and transmembrane pH gradient in the acidophile Thiobacillus ferro-oxidans. Biochem. J. 178, 195–100 (1979). A demonstration of the PMF parameters for an extreme acidophile.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Matin, A. pH homeostasis in acidophiles. Novartis Found. Symp. 221, 152–163 (1999).

    CAS  PubMed  Google Scholar 

  115. Michels, M. & Bakker, E. P. Generation of a large, protonophore-sensitive proton motive force and pH difference in the acidophilic bacteria Thermoplasma acidophilum and Bacillus acidocaldarius. J. Bacteriol. 161, 231–237 (1985).

    CAS  PubMed  PubMed Central  Google Scholar 

  116. Wakai, S., Ohmori, A., Kanao, T., Sugio, T. & Kamimura, K. Purification and biochemical characterization of the F1-ATPase from Acidithiobacillus ferrooxidans NASF-1 and analysis of the atp operon. Biosci. Biotechnol. Biochem. 69, 1884–1891 (2005).

    Article  CAS  PubMed  Google Scholar 

  117. Hamamoto, T. et al. Characterization of a gene responsible for the Na+/H+ antiporter system of alkalophilic Bacillus species strain C-125. Mol. Microbiol. 14, 939–946 (1994). This investigation of non-alkaliphilic, antiporter-negative mutants results in the identification of genes encoding part of an Mrp-type antiporter that is central to pH homeostasis of alkaliphilic Bacillus spp.

    Article  CAS  PubMed  Google Scholar 

  118. Krulwich, T. A. Alkaliphiles: 'basic' molecular problems of pH tolerance and bioenergetics. Mol. Microbiol. 15, 403–410 (1995).

    Article  CAS  PubMed  Google Scholar 

  119. Krulwich, T. A., Hicks, D. B., Swartz, T. H. & Ito, M. in Physiology and Biochemistry of Extremophiles (eds Gerday, C. & Glansdorff, N.) 311–329 (ASM Press, Washington, 2007).

    Book  Google Scholar 

  120. Sturr, M. G., Guffanti, A. A. & Krulwich, T. A. Growth and bioenergetics of alkaliphilic Bacillus firmus OF4 in continuous culture at high pH. J. Bacteriol. 176, 3111–3116 (1994). This study of PMF parameters, cytoplasmic pH and growth rates at pH values from pH 7.5 to pH >11.0 demonstrates the robust pH homeostatic capacity of alkaliphilic B. pseudofirmus OF4 and its ability to grow, after exceeding that capacity, with a cytoplasmic pH as high as 9.5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Zilberstein, D., Agmon, V., Schuldiner, S. & Padan, E. Escherichia coli intracellular pH, membrane potential, and cell growth. J. Bacteriol. 158, 246–252 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. Mathiesen, C. & Hagerhall, C. The 'antiporter module' of respiratory chain Complex I includes the MrpC/NuoK subunit — a revision of the modular evolution scheme. FEBS Lett. 5459, 7–13 (2003).

    Article  CAS  Google Scholar 

  123. Swartz, T. H., Ikewada, S., Ishikawa, O., Ito, M. & Krulwich, T. A. The Mrp system: a giant among monovalent cation/proton antiporters? Extremophiles 9, 345–354 (2005).

    Article  CAS  PubMed  Google Scholar 

  124. Kajiyama, Y., Otagiri, M., Sekiguchi, J., Kudo, T. & Kosono, S. The MrpA, MrpB and MrpD subunits of the Mrp antiporter complex in Bacillus subtilis contain membrane-embedded and essential acidic residues. Microbiology 155, 2137–2147 (2009).

    Article  CAS  PubMed  Google Scholar 

  125. Morino, M. et al. Single site mutations in the hetero-oligomeric Mrp antiporter from alkaliphilic Bacillus pseudofirmus OF4 that affect Na+/H+ antiport activity, sodium exclusion, individual Mrp protein levels or Mrp complex formation. J. Biol. Chem. 285, 30942–30950 (2010). A large panel of site-directed mutations in the Mrp system genes from an alkaliphile include those that affect the membrane levels and activity profile of the system that or selectively affect the formation of Mrp hetero-oligomers of two sizes.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Morino, M., Natsui, S., Swartz, T. H., Krulwich, T. A. & Ito, M. Single gene deletions of mrpA to mrpG and mrpE point mutations affect activity of the Mrp Na+/H+ antiporter of alkaliphilic Bacillus and formation of hetero-oligomeric Mrp complexes. J. Bacteriol. 190, 4162–4172 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Kajiyama, Y., Otagiri, M., Sekiguchi, J., Kosono, S. & Kudo, T. Complex formation by the mrpABCDEFG gene products, which constitute a principal Na+/H+ antiporter in Bacillus subtilis. J. Bacteriol. 189, 7511–7514 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Fujinami, S. et al. The voltage-gated Na+ channel NaVBP co-localizes with methyl-accepting chemotaxis protein at cell poles of alkaliphilic Bacillus pseudofirmus OF4. Microbiology 153, 4027–4038 (2007).

    Article  CAS  PubMed  Google Scholar 

  129. Ito, M. et al. MotPS is the stator-force generator for motility of alkaliphilic Bacillus and its homologue is a second functional Mot in Bacillus subtilis. Mol. Microbiol. 53, 1035–1049 (2004).

    Article  CAS  PubMed  Google Scholar 

  130. Ito, M. et al. The voltage-gated Na+ channel NavBP has a role in motility, chemotaxis, and pH homeostasis of an alkaliphilic Bacillus. Proc. Natl Acad. Sci. USA 101, 10566–10571 (2004). This study reveals the role of a bacterial voltage-gated Na+ channel in supporting the re-entry of Na+ to support Na+/H+ antiport-dependent pH homeostasis in an alkaliphilic Bacillus species.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Krulwich, T. A., Federbush, J. G. & Guffanti, A. A. Presence of a nonmetabolizable solute that is translocated with Na+ enhances Na+-dependent pH homeostasis in an alkalophilic Bacillus. J. Biol. Chem. 260, 4055–4058 (1985).

    CAS  PubMed  Google Scholar 

  132. Krulwich, T. A., Hicks, D. B. & Ito, M. Cation/proton antiporter complements of bacteria: why so large and diverse? Mol. Microbiol. 74, 257–260 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Ferguson, S. A., Keis, S. & Cook, G. M. Biochemical and molecular characterization of a Na+-translocating F1Fo-ATPase from the thermoalkaliphilic bacterium Clostridium paradoxum. J. Bacteriol. 188, 5045–5054 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Fujisawa, M., Fackelmayer, O., Liu, J., Krulwich, T. A. & Hicks, D. B. The ATP synthase a-subunit of extreme alkaliphiles is a distinct variant. J. Biol. Chem. 285, 32105–32115 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Ivey, D. M. & Krulwich, T. A. Two unrelated alkaliphilic Bacillus species possess identical deviations in sequence from those of other prokaryotes in regions of F0 proposed to be involved in proton translocation through the ATP synthase. Res. Microbiol. 143, 467–470 (1992).

    Article  CAS  PubMed  Google Scholar 

  136. Liu, J., Fujisawa, M., Hicks, D. B. & Krulwich, T. A. Characterization of the functionally critical AXAXAXA and PXXEXXP motifs of the ATP synthase c-subunit from an alkaliphilic Bacillus. J. Biol. Chem. 284, 8714–8725 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Wang, Z., Hicks, D. B., Guffanti, A. A., Baldwin, K. & Krulwich, T. A. Replacement of amino acid sequence features of a- and c-subunits of ATP synthases of alkaliphilic Bacillus with the Bacillus consensus sequence results in defective oxidative phosphorylation and non-fermentative growth at pH 10.5. J. Biol. Chem. 279, 26546–26554 (2004). The first demonstration that chromosomal mutations which change alkaliphile-specific motifs of the ATP synthase of an extreme alkaliphile result in suboptimal ATP synthesis and deficient non-fermentative growth at high pH.

    Article  CAS  PubMed  Google Scholar 

  138. Preiss, L., Yildiz, Ö., Hicks, D., Krulwich, T. A. & Meier, T. A new type of proton coordination in an F1F0-ATP synthase rotor ring. PLoS Biol. 8, e1000443 (2010). The crystal structure of the ATP synthase rotor of alkaliphilic B. pseudofirmus OF4 reveals features of proton coordination that are in part adaptations to support successful ATP synthesis coupled to proton passage into the cytoplasm at high external pH.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  139. Kashket, E. R. The proton motive force in bacteria: a critical assessment of methods. Annu. Rev. Microbiol. 39, 219–242 (1985).

    Article  CAS  PubMed  Google Scholar 

  140. Mitchell, P. Coupling of phosphorylation to electron and hydrogen transfer by a chemiosmotic type of mechanism. Nature 191, 144–148 (1961).

    Article  CAS  PubMed  Google Scholar 

  141. Rottenberg, H. The measurement of membrane potential and ΔpH in cells, organelles, and vesicles. Methods Enzymol. 55, 547–569 (1979).

    Article  CAS  PubMed  Google Scholar 

  142. Zilberstein, D., Schuldiner, S. & Padan, E. Proton electrochemical gradient in Escherichia coli cells and its relation to active transport of lactose. Biochemistry 18, 669–673 (1979).

    Article  CAS  PubMed  Google Scholar 

  143. Guffanti, A. A. & Hicks, D. B. Molar growth yields and bioenergetic parameters of extremely alkaliphilic Bacillus species in batch cultures, and growth in a chemostat at pH 10.5. J. Gen. Microbiol. 137, 2375–2379 (1991).

    Article  CAS  PubMed  Google Scholar 

  144. Shioi, J. I., Imae, Y. & Oosawa, F. Protonmotive force and motility of Bacillus subtilis. J. Bacteriol. 133, 1083–1038 (1978).

    CAS  PubMed  PubMed Central  Google Scholar 

  145. Guffanti, A. A., Susman, P., Blanco, R. & Krulwich, T. A. The protonmotive force and α-aminoisobutyric acid transport in an obligately alkalophilic bacterium. J. Biol. Chem. 253, 708–715 (1978).

    CAS  PubMed  Google Scholar 

  146. Tsujimoto, K., Semadeni, M., Huflejt, M. & Packer, L. Intracellular pH of halobacteria can be determined by the fluorescent dye 2′, 7′-bis(carboxyethyl)-5(6)-carboxyfluorescein. Biochem. Biophys. Res. Commun. 155, 123–129 (1988).

    Article  CAS  PubMed  Google Scholar 

  147. Schade, C., Flemstrom, G. & Holm, L. Hydrogen ion concentration in the mucus layer on top of acid-stimulated and -inhibited rat gastric mucosa. Gastroenterology 107, 180–188 (1994).

    Article  CAS  PubMed  Google Scholar 

  148. Baumgartner, H. K. & Montrose, M. H. Regulated alkali secretion acts in tandem with unstirred layers to regulate mouse gastric surface pH. Gastroenterology 126, 774–783 (2004).

    Article  CAS  PubMed  Google Scholar 

  149. Henriksnas, J. et al. Impaired mucus-bicarbonate barrier in Helicobacter pylori-infected mice. Am. J. Physiol. Gastrointest. Liver Physiol. 291, G396–G403 (2006).

    Article  CAS  Google Scholar 

  150. Scott, D. R., Marcus, E. A., Wen, Y., Oh, J. & Sachs, G. Gene expression in vivo shows that Helicobacter pylori colonizes an acidic niche on the gastric surface. Proc. Natl Acad. Sci. USA 104, 7235–7240 (2007). The first paper to elucidate the in vivo transcriptome of H. pylori , supporting indications that the natural environment of this gastric pathogen is acidic with the finding that many acid acclimation genes have increased expression when compared with their expression in vitro at neutral pH.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

T.A.K. is supported by a research grant from the US National Institutes of Health. G.S. is supported by grants from the US National Institutes of Health and the United States Veterans Administration. E.P. is supported by grants from the USA–Israel Bi-National Science Foundation and from the European Drug Initiative on Channels and Transporters. We thank colleagues L. Kozachkov for help with figure 2; M. Ito, J. Liu, M. Morino and L. Preiss for their assistance with panels of figure 4; and D. B. Hicks, H. R. Kaback, J. Kraut, T. Meier, L. Preiss, D. R. Scott, O. Vagin and Y. Wen for critically reviewing sections of the manuscript.

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  1. Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, Box 1603, 1 Gustave L. Levy Place, New York, 10029, New York, USA

    Terry A. Krulwich

  2. Departments of Physiology and Medicine, David Geffen School of Medicine at the University of California, Los Angeles, 405 Hilgard Ave., Los Angeles, 90024, California, USA

    George Sachs

  3. Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, 91904, Israel

    Etana Padan

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Glossary

Proton motive force

(PMF). A transmembrane electrochemical gradient across the bacterial cell membrane.

Acidophilic bacteria

Bacteria that can grow at a low external pH; extreme acidophiles can grow at an external pH of <3.0, whereas the lowest growth pH for moderate acidophiles is in the pH 3.0–5.0 range.

Alkaliphilic bacteria

Bacteria that can grow at a high external pH; extremely alkaliphilic bacteria grow at an external pH of ≥10.0, whereas moderate alkaliphiles grow in the pH 9.0–10.0 range. The pH range for growth of facultative alkaliphiles extends down to pH 7.0–7.5.

Alkaline soda lakes

Highly alkaline lakes that are rich in dissolved sodium salts, especially sodium carbonate, sodium chloride and sodium sulphate. These lakes are found in many parts of the world.

Groundwaters

Waters that collect below the surface of the Earth, filling the porous spaces in soil, rocks and sediment.

Extremophiles

Organisms that grow under conditions (for example, pH, temperature, salt concentration, pressure, etc.) that are incompatible with growth for most organisms.

Cytoplasmic buffering capacity

The capacity of the cytoplasmic contents to resist changes in pH on exposure to an acid or a base (that is, molecules possessing acidic or basic groups with pK values in the range of the challenge pH).

pI profiles

The relative representation of proteins (as predicted by the genome sequence) that have different pI values (isoelectric points, at which the protein has no net charge).

Two component systems

(TCSs). Protein systems that are usually composed of two multidomain proteins — a sensory histidine kinase and a response regulator — that sense and initiate a response to a stimulus such as a pH change. The localization of the sensory domain can support sensing of either external pH or cytoplasmic pH.

Discontinuous helices

Membrane-spanning helical protein segments that are interrupted in the middle by an extended non-helical region.

K m

Michaelis constant, an important characteristic of the enzyme–substrate interaction. It reflects the concentration of substrate at which half the active sites of an enzyme are filled. For transport reactions, the term apparent Km is used.

Cysteine-less protein

A protein that has had all the native cysteines replaced with other residues. If such a protein is active, it is useful for a range of structure–function experiments.

Multiconformation continuum electrostatics

A simulation program that uses a combination of biophysical approaches to calculate properties that facilitate the development of functional models.

pK

A property of a basic or acidic group that is related to the equilibrium constant of its ionization and is defined as the pH at which the group is half dissociated.

Acid acclimation

The ability of a Gram-negative neutralophile to maintain a periplasmic pH of close to neutral in highly acidic media, allowing both survival and growth.

Chemolithotrophic bacteria

Bacteria that can apply oxidation–reduction reactions to inorganic compounds to provide all the energy that they need for cell growth and maintenance processes.

ω-alicyclic fatty acid

Fatty acids with rings at the end.

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Krulwich, T., Sachs, G. & Padan, E. Molecular aspects of bacterial pH sensing and homeostasis. Nat Rev Microbiol 9, 330–343 (2011). https://doi.org/10.1038/nrmicro2549

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