Gain-of-function mutations cluster in distinct regions associated with the signalling pathway in the PAS domain of the aerotaxis receptor, Aer

Molecular Microbiology

Volumn 77, Issue 3, 2010, Pages 575-586

  Campbell, Asharie J ^a   Watts, Kylie J ^a   Johnson, Mark S ^a   Taylor, Barry L ^a  

^a LOMA LINDA UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AER RECEPTOR; FLAVINE ADENINE NUCLEOTIDE; PAS PROTEIN; PROTEIN; RECEPTOR; SCAFFOLD PROTEIN; UNCLASSIFIED DRUG; AER PROTEIN, E COLI; CARRIER PROTEIN; ESCHERICHIA COLI PROTEIN; PROTEIN BINDING;

ARTICLE; AZOTOBACTER VINELANDII; BINDING SITE; CONTROLLED STUDY; ESCHERICHIA COLI; GENE CLUSTER; GENE MAPPING; GENE MUTATION; GENETIC CODE; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; AMINO ACID SEQUENCE; CHEMISTRY; CONFORMATION; GENETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

AZOTOBACTER VINELANDII; ESCHERICHIA COLI;

AMINO ACID SEQUENCE; CARRIER PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FLAVIN-ADENINE DINUCLEOTIDE; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SIGNAL TRANSDUCTION;

EID: 77954839079     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2010.07231.x     Document Type: Article

References (42)

1. Ames, P., Studdert, C. A., Reiser, R. H. Parkinson, J. S. (2002) Collaborative signaling by mixed chemoreceptor teams in Escherichia coli. Proc Natl Acad Sci USA 99 : 7060 7065.
2. Amin, D. N., Taylor, B. L. Johnson, M. S. (2006) Topology and boundaries of the aerotaxis receptor Aer in the membrane of Escherichia coli. J Bacteriol 186 : 894 901.
3. Amin, D. N., Taylor, B. L. Johnson, M. S. (2007) Organization of the aerotaxis receptor Aer in the membrane of Escherichia coli. J Bacteriol 189 : 7206 7212.
4. Aravind, L. Ponting, C. P. (1999) The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins. FEMS Microbiol Lett 176 : 111 116.
5. Bibikov, S. I., Barnes, L. A., Gitin, Y. Parkinson, J. S. (2000) Domain organization and flavin adenine dinucleotide-binding determinants in the aerotaxis signal transducer Aer of Escherichia coli. Proc Natl Acad Sci USA 97 : 5830 5835.
6. Borgstahl, G. E., Williams, D. R. Getzoff, E. D. (1995) 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Biochemistry 34 : 6278 6287.
7. Burón-Barral, M. C., Gosink, K. K. Parkinson, J. S. (2006) Loss- and gain-of-function mutations in the F1-HAMP region of the Escherichia coli aerotaxis transducer Aer. J Bacteriol 188 : 3477 3486.
8. Campbell, A. J. (2010) Structural Dynamics and Signaling Roles of the Aer PAS and F1 Regions. PhD Dissertation, Division of Microbiology and Molecular Genetics, Loma Linda University
9. Chang, A. C. Cohen, S. N. (1978) Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol 134 : 1141 1156.
10. Edwards, J. C., Johnson, M. S. Taylor, B. L. (2006) Differentiation between electron transport sensing and proton motive force sensing by the Aer and Tsr receptors for aerotaxis. Mol Microbiol 62 : 823 837.
11. Etzkorn, M., Kneuper, H., Dunnwald, P., Vijayan, V., Kramer, J., Griesinger, C., et al. (2008) Plasticity of the PAS domain and a potential role for signal transduction in the histidine kinase DcuS. Nat Struct Mol Biol 15 : 1031 1039.
12. Gong, W., Hao, B., Mansy, S. S., Gonzalez, G., Gilles-Gonzalez, M. A. Chan, M. K. (1998) Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction. Proc Natl Acad Sci USA 95 : 15177 15182.
13. Gosink, K. K., Burón-Barral, M. C. Parkinson, J. S. (2006) Signaling interactions between the aerotaxis transducer Aer and heterologous chemoreceptors in Escherichia coli. J Bacteriol 188 : 3487 3493.
14. Harigai, M., Imamoto, Y., Kamikubo, H., Yamazaki, Y. Kataoka, M. (2003) Role of an N-terminal loop in the secondary structural change of photoactive yellow protein. Biochemistry 42 : 13893 13900.
15. Hazelbauer, G. L., Falke, J. J. Parkinson, J. S. (2008) Bacterial chemoreceptors: high-performance signaling in networked arrays. Trends Biochem Sci 33 : 9 19.
16. Herrmann, S., Ma, Q., Johnson, M. S., Repik, A. V. Taylor, B. L. (2004) PAS domain of the Aer redox sensor requires C-terminal residues for native-fold formation and flavin adenine dinucleotide binding. J Bacteriol 186 : 6782 6791.
17. Huang, Z. J., Edery, I. Rosbash, M. (1993) PAS is a dimerization domain common to Drosophila period and several transcription factors. Nature 364 : 259 262.
18. Hulko, M., Berndt, F., Gruber, M., Linder, J. U., Truffault, V., Schultz, A., et al. (2006) The HAMP domain structure implies helix rotation in transmembrane signaling. Cell 126 : 929 940.
19. Jung, K. H. Spudich, J. L. (1998) Suppressor mutation analysis of the sensory rhodopsin I-transducer complex: insights into the color-sensing mechanism. J Bacteriol 180 : 2033 2042.
20. Kay, S. A. (1997) PAS, present, and future: clues to the origins of circadian clocks. Science 276 : 753 754.
21. Kewley, R. J., Whitelaw, M. L. Chapman-Smith, A. (2004) The mammalian basic helix-loop-helix/PAS family of transcriptional regulators. Int J Biochem Cell Biol 36 : 189 204.
22. Key, J. Moffat, K. (2005) Crystal structures of deoxy and CO-bound bjFixLH reveal details of ligand recognition and signaling. Biochemistry 44 : 4627 4635.
23. Key, J., Hefti, M., Purcell, E. B. Moffat, K. (2007) Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: signaling, dimerization, and mechanism. Biochemistry 46 : 3614 3623.
24. Kiefer, F., Arnold, K., Kunzli, M., Bordoli, L. Schwede, T. (2009) The SWISS-MODEL Repository and associated resources. Nucleic Acids Res 37 : D387 D392.
25. Nambu, J. R., Lewis, J. O., Wharton, K. A., Jr. Crews, S. T. (1991) The Drosophila single-minded gene encodes a helix-loop-helix protein that acts as a master regulator of CNS midline development. Cell 67 : 1157 1167.
26. Park, S. Y., Borbat, P. P., Gonzalez-Bonet, G., Bhatnagar, J., Pollard, A. M., Freed, J. H., et al. (2006) Reconstruction of the chemotaxis receptor-kinase assembly. Nat Struct Mol Biol 13 : 400 407.
27. Parkinson, J. S. (1978) Complementation analysis and deletion mapping of Escherichia coli mutants defective in chemotaxis. J Bacteriol 135 : 45 53.
28. Pellequer, J. L., Wager-Smith, K. A., Kay, S. A. Getzoff, E. D. (1998) Photoactive yellow protein: a structural prototype for the three-dimensional fold of the PAS domain superfamily. Proc Natl Acad Sci USA 95 : 5884 5890.
29. Rebbapragada, A., Johnson, M. S., Harding, G. P., Zuccarelli, A. J., Fletcher, H. M., Zhulin, I. B. Taylor, B. L. (1997) The Aer protein and the serine chemoreceptor Tsr independently sense intracellular energy levels and transduce oxygen, redox, and energy signals for Escherichia coli behavior. Proc Natl Acad Sci USA 94 : 10541 10546.
30. Repik, A., Rebbapragada, A., Johnson, M. S., Haznedar, J. O., Zhulin, I. B. Taylor, B. L. (2000) PAS domain residues involved in signal transduction by the Aer redox sensor of Escherichia coli. Mol Microbiol 36 : 806 816.
31. Taylor, B. L. (2007) Aer on the inside looking out: paradigm for a PAS-HAMP role in sensing oxygen, redox and energy. Mol Microbiol 65 : 1415 1424.
32. Taylor, B. L. Zhulin, I. B. (1999) PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol Mol Biol Rev 63 : 479 506.
33. Taylor, B. L., Zhulin, I. B. Johnson, M. S. (1999) Aerotaxis and other energy-sensing behavior in bacteria. Annu Rev Microbiol 53 : 103 128.
34. Taylor, B. L., Watts, K. J. Johnson, M. S. (2007) Oxygen and redox sensing by two-component systems that regulate behavioral responses: behavioral assays and structural studies of aer using in vivo disulfide cross-linking. Methods Enzymol 422 : 190 232.
35. Ukaegbu, U. E. Rosenzweig, A. C. (2009) Structure of the Redox Sensor Domain of Methylococcus capsulatus (Bath) MmoS. Biochemistry 48 : 2207 2215.
36. Vanhercke, T., Ampe, C., Tirry, L. Denolf, P. (2005) Reducing mutational bias in random protein libraries. Anal Biochem 339 : 9 14.
37. Watts, K. J., Ma, Q., Johnson, M. S. Taylor, B. L. (2004) Interactions between the PAS and HAMP domains of the Escherichia coli aerotaxis receptor Aer. J Bacteriol 186 : 7440 7449.
38. Watts, K. J., Sommer, K., Fry, S. L., Johnson, M. S. Taylor, B. L. (2006) Function of the N-terminal cap of the PAS domain in signaling by the aerotaxis receptor Aer. J Bacteriol 188 : 2154 2162.
39. Xie, Z., Ulrich, L. E., Zhulin, I. B. Alexandre, G. (2010) PAS domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis. Proc Natl Acad Sci USA 107 : 2235 2240.
40. Yu, H. S., Saw, J. H., Hou, S., Larsen, R. W., Watts, K. J., Johnson, M. S., et al. (2002) Aerotactic responses in bacteria to photoreleased oxygen. FEMS Microbiol Lett 217 : 237 242.
41. Zhulin, I. B., Johnson, M. S. Taylor, B. L. (1997) How do bacteria avoid high oxygen concentrations? Biosci Rep 17 : 335 342.
42. Zoltowski, B. D., Schwerdtfeger, C., Widom, J., Loros, J. J., Bilwes, A. M. Crane, B. R. (2007) Conformational switching in the fungal light sensor Vivid. Science 316 : 1054 1057.