Termination and antitermination: RNA polymerase runs a stop sign

Nature Reviews Microbiology

Volumn 9, Issue 5, 2011, Pages 319-329

  Santangelo, Thomas J ^a   Artsimovitch, Irina ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEGESTROL ACETATE; RNA POLYMERASE;

ANTICODON; ARTICLE; BACTERIOPHAGE; BACTERIOPHAGE LAMBDA; BACTERIUM; ESCHERICHIA COLI; GENE EXPRESSION; NONHUMAN; PRIORITY JOURNAL; RIBOSOME; RNA BINDING; RNA TRANSLATION; SIGNAL TRANSDUCTION; STOP CODON; THERMUS THERMOPHILUS;

BACTERIA; BACTERIAL PROTEINS; BACTERIOPHAGES; DNA-DIRECTED RNA POLYMERASES; RIBOSOMES; RNA, TRANSFER; RNA-BINDING PROTEINS; TERMINATOR REGIONS, GENETIC; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS);

EID: 79954597274     PISSN: 17401526     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrmicro2560     Document Type: Article

References (67)

1. + antiporter of Escherichia coli. J. Biol. Chem. 279, 3265-3272 (2004). (Pubitemid 38140560)
2. + antiporter of Escherichia coli at physiological pH. J. Biol. Chem. 283, 15975-15987 (2008).
3. + antiporter of Escherichia coli, at physiological pH. Biochemistry 46, 2419-2430 (2007). (Pubitemid 46362416)
4. + antiporter of Escherichia coli with functional implications. Proc. Natl Acad. Sci. USA 103, 2629-2634 (2006).
5. 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). (Pubitemid 46910566)
6. 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). (Pubitemid 47206406)
7. 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). (Pubitemid 27079746)
8. 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).
9. 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). (Pubitemid 351251719)
10. 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). (Pubitemid 33078384)
11. 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). (Pubitemid 35449269)
12. +-gated urea channel: the link between Helicobacter pylori urease and gastric colonization. Science 287, 482-485 (2000).
13. 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). (Pubitemid 30056496)
14. Weeks, D. & Sachs, G. Sites of pH regulation of the urea channel of Helicobacter pylori. Mol. Microbiol. 40, 1249-1259 (2001). (Pubitemid 32635296)
15. +, is necessary for acid survival of Helicobacter pylori. J. Bacteriol. 192, 94-103 (2010).
16. 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).
17. Beier, D. & Frank, R. Molecular characterization of two-component systems of Helicobacter pylori. J. Bacteriol. 182, 2068-2076 (2000). (Pubitemid 30183523)
18. 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). (Pubitemid 37070788)
19. 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).
20. Pflock, M., Kennard, S., Finsterer, N. & Beier, D. Acid-responsive gene regulation in the human pathogen Helicobacter pylori. J. Biotechnol. 126, 52-60 (2006). (Pubitemid 44402773)
21. 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).
22. Hong, W. et al. Medium pH-dependent redistribution of the urease of Helicobacter pylori. J. Med. Microbiol. 52, 211-216 (2003). (Pubitemid 36324207)
23. 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). (Pubitemid 36076254)
24. 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).
25. Johnson, D. B. in Physiology and Biochemistry of Extremophiles (eds Gerday, C. & Glansdorff, N.) 257-270 (ASM Press, Washington, 2007).
26. 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).
27. 1 complex? Biochim. Biophys. Acta 1555, 37-43 (2002). (Pubitemid 35246002)
28. Valdes, J. et al. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9, 597 (2008).
29. 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).
30. 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).
31. Matin, A. pH homeostasis in acidophiles. Novartis Found. Symp. 221, 152-163 (1999).
32. 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). (Pubitemid 15156123)
33. 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). (Pubitemid 41558852)
34. + antiporter system of alkalophilic Bacillus species strain C-125. Mol. Microbiol. 14, 939-946 (1994) (Pubitemid 24376131)
35. Krulwich, T. A. Alkaliphiles: 'basic' molecular problems of pH tolerance and bioenergetics. Mol. Microbiol. 15, 403-410 (1995).
36. 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).
37. 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). (Pubitemid 24166699)
38. Zilberstein, D., Agmon, V., Schuldiner, S. & Padan, E. Escherichia coli intracellular pH, membrane potential, and cell growth. J. Bacteriol. 158, 246-252 (1984). (Pubitemid 14125217)
39. 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). (Pubitemid 36959834)
40. 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). (Pubitemid 41428347)
41. 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).
42. + antiport activity, sodium exclusion, individual Mrp protein levels or Mrp complex formation. J. Biol. Chem. 285, 30942-30950 (2010).
43. + antiporter of alkaliphilic Bacillus and formation of hetero-oligomeric Mrp complexes. J. Bacteriol. 190, 4162-4172 (2008). (Pubitemid 351812862)
44. + antiporter in Bacillus subtilis. J. Bacteriol. 189, 7511-7514 (2007). (Pubitemid 47557369)
45. VBP co-localizes with methyl-accepting chemotaxis protein at cell poles of alkaliphilic Bacillus pseudofirmus OF4. Microbiology 153, 4027-4038 (2007).
46. 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). (Pubitemid 39120427)
47. vBP has a role in motility, chemotaxis, and pH homeostasis of an alkaliphilic Bacillus. Proc. Natl Acad. Sci. USA 101, 10566-10571 (2004). (Pubitemid 38955782)
48. +-dependent pH homeostasis in an alkalophilic Bacillus. J. Biol. Chem. 260, 4055-4058 (1985). (Pubitemid 15096473)
49. 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).
50. o-ATPase from the thermoalkaliphilic bacterium Clostridium paradoxum. J. Bacteriol. 188, 5045-5054 (2006). (Pubitemid 44051471)
51. 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).
52. 0 proposed to be involved in proton translocation through the ATP synthase. Res. Microbiol. 143, 467-470 (1992).
53. 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).
54. 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). (Pubitemid 38798810)
55. 0-ATP synthase rotor ring. PLoS Biol. 8, e1000443 (2011)
56. Kashket, E. R. The proton motive force in bacteria: a critical assessment of methods. Annu. Rev. Microbiol. 39, 2 19-242 (1985).
57. Mitchell, P. Coupling of phosphorylation to electron and hydrogen transfer by a chemiosmotic type of mechanism. Nature 191, 144-148 (1961).
58. Rottenberg, H. The measurement of membrane potential and ΔpH in cells, organelles, and vesicles. Methods Enzymol. 55, 547-569 (1979).
59. 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).
60. 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).
61. Shioi, J. I., Imae, Y & Oosawa, F Protonmotive force and motility of Bacillus subtilis. J. Bacteriol. 133, 1083-1038 (1978).
62. 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). (Pubitemid 8271444)
63. 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).
64. 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). (Pubitemid 24195360)
65. 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). (Pubitemid 38298326)
66. Henriksnas, J. et al. Impaired mucus-bicarbonate barrier in Helicobacter pylori-infected mice. Am. J. Physiol. Gastrointest. Liver Physiol. 291, G396-G403 (2006). (Pubitemid 44330159)
67. 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). (Pubitemid 47186038)