Properties of HflX, an enigmatic protein from escherichia coli

Journal of Bacteriology

Volumn 191, Issue 7, 2009, Pages 2307-2314

  Dutta, Dipak ^a,c   Bandyopadhyay, Kaustav ^a   Datta, Ajit Bikram ^a,d   Sardesai, Abhijit A ^b   Parrack, Pradeep ^a  

^a BOSE INSTITUTE   (India)

^b CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS   (India)

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

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ESCHERICHIA COLI PROTEIN; GUANINE NUCLEOTIDE BINDING PROTEIN; GUANOSINE TRIPHOSPHATASE; HFLC PROTEIN; HFLK PROTEIN; HFLX PROTEIN; UNCLASSIFIED DRUG; HFLX PROTEIN, E COLI;

ARTICLE; BACTERIAL MUTATION; COLIPHAGE; CONTROLLED STUDY; ENZYME ACTIVITY; ESCHERICHIA COLI; LYSOGENIZATION; MUTATIONAL ANALYSIS; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; BACTERIOPHAGE LAMBDA; CHEMISTRY; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; PHYSIOLOGY; VIROLOGY;

BACTERIA (MICROORGANISMS); ENTEROBACTERIA PHAGE LAMBDA; ESCHERICHIA COLI;

ADENOSINE TRIPHOSPHATASES; BACTERIOPHAGE LAMBDA; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GTP PHOSPHOHYDROLASES; GTP-BINDING PROTEINS; LYSOGENY;

EID: 64049097151     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01353-08     Document Type: Article

References (56)

1. Andrade, M. A., P. Chacon, J. J. Merelo, and F. Moran. 1993. Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network. Protein Eng. 6:383-390.
2. Arvidson, C. G., and M. So. 1997. Isolation and biochemical characterization of the PilA protein of Neisseria meningitides. Arch. Biochem. Biophys. 348: 357-362.
3. Banuett, F., and I. Herskowitz. 1987. Identification of polypeptides encoded by an Escherichia coli locus (hflA) that governs the lysis-lysogeny decision of bacteriophage lambda. J. Bacteriol. 169:4076-4085.
4. Banuett, F., M. A. Hoyt, L. Mcfarlane, H. Echols, and I. Herskowitz. 1986. HflB, a new locus regulating lysogeny and the level of bacteriophage lambda CII protein. J. Mol. Biol. 187:213-224.
5. Belfort, M., and D. L. Wulff. 1971. A mutant of Escherichia coli that is lysogenized with high frequency, p. 739-742. In A. D. Hershey (ed.), The bacteriophage lambda. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
6. Bohm, G., R. Muhr, and E. Jaenicke. 1992. Quantitative analysis of protein far UV circular dichroism spectra by neural networks. Protein Eng. 5:191- 195.
7. Bourne, H. R., D. A. Sanders, and F. McCormick. 1990. The GTPase superfamily: a conserved switch for diverse cell functions. Nature 348:125-132.
8. Bourne, H. R., D. A. Sanders, and F. McCormick. 1991. The GTPase superfamily: conserved structure and molecular mechanism. Nature 349:117-127.
9. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
10. Bryson, K., L. J. McGuffin, R. L. Marsden, J. J. Ward, S. Sodhi, and D. T. Jones. 2005. Protein structure prediction servers at University College London. Nucleic Acids Res. 33:W36-W38.
11. Caillet, J., and L. Droogmans. 1988. Molecular cloning of the Escherichia coli miaA gene involved in the formation of delta 2-isopentenyl adenosine in tRNA. J. Bacteriol. 170:4147-4152.
12. Cherepanov, P. P., and W. Wackernagel. 1995. Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. Gene 158:9-14.
13. Chuang, S. E., and F. R. Blattner. 1993. Characterization of twenty-six new heat shock genes of Escherichia coli. J. Bacteriol. 175:5242-5252.
14. Connolly, D. M., and M. E. Winkler. 1989. Genetic and physiological relationships among the miaA gene, 2-methylthio-N6-(delta 2-isopentenyl)- adenosine tRNA modification, and spontaneous mutagenesis in Escherichia coli K-12. J. Bacteriol. 171:3233-3246.
15. Coros, A. M., E. Twiss, N. P. Tavakoli, and K. M. Derbyshire. 2005. Genetic Evidence that GTP is required for transposition of IS903 and Tn552 in Escherichia coli. J. Bacteriol. 187:4598-4606.
16. Court, D. L., A. B. Oppenheim, and S. L. Adhya. 2007. A new look at bacteriophage λ genetic networks. J. Bacteriol. 189:298-304.
17. Cuff, J. A., M. E. Clamp, A. S. Siddiqui, M. Finlay, and G. J. Barton. 1998. Jpred: a consensus secondary structure prediction server. Bioinformatics 14:892-893.
18. Daigle, D. M., L. Rossi, A. M. Berghuis, L. Arvind, E. V. Konnin, and E. D. Brown. 2002. YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permutated G-motifs and marked burst kinetics. Biochemistry 41:11109-11117.
19. Datsenko, K. A., and B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97:6640-6645.
20. Dutta, D. 2006. Studies on the protein HflX from Escherichia coli: searching for its function. Ph.D. dissertation. Jadavpur University, Kolkata, India.
21. Echols, H. 1986. Bacteriophage λ development: temporal switches and the choice of lysis or lysogeny. Trends Genet. 2:26-30.
22. Engels, S., C. Ludwig, J. E. Schweitzer, C. Mack, M. Bott, and S. Schaffer. 2005. The transcriptional activator ClgR controls transcription of genes involved in proteolysis and DNA repair in Corynebacterium glutamicam. Mol. Microbiol. 57:576-591.
23. Gasteiger, E., C. Hoogland, A. Gattiker, S. Duvaud, M. R. Wilkins, R. D. Appel, and A. Bairoch. 2005. Protein identification and analysis tools on the ExPASy server, p. 571-607. In J. M. Walker (ed.),The proteomics protocols handbook. Humana Press, Totowa, NJ.
24. Geissmann, T. A., and D. Touati. 2004. Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator. EMBO J. 23:396-405.
25. Herman, C., T. Ogura, T. Tomoyasu, S. Hiraga, Y. Akiyama, K. Ito, R. Thomas, R. D'Ari, and P. Bouloc. 1993. Cell growth and λ phage development controlled by the same essential Escherichia coli gene, ftsH/hflB. Proc. Natl. Acad. Sci. USA 90:10861-10865.
26. Herskowitz, I., and D. Hagen. 1980. The lysis-lysogeny decision of phage -: explicit programming and responsiveness. Annu. Rev. Genet. 14:399-445.
27. Hoyt, M. A., D. M. Knight, A. Das, H. I. Miller, and H. Echols. 1982. Control of phage lambda development by stability and synthesis of cII protein: role of the viral cIII and host hflA, himA and himD genes. Cell 31:565-573.
28. Jain, N., N. Dhimole, A. R. Khan, D. De, S. K. Tomar, M. Sajish, D. Dutta, P. Parrack, and B. Prakash. 25 December 2008, posting date. E. coli HflX interacts with 50S ribosomal subunits in presence of nucleotides. Biochem. Biophys. Res. Commun. doi:10.1016/j.bbrc.2008.12.072.
29. Kajitani, M., A. Kato, A. Wada, Y. Inokuchi, and A. Ishihama. 1994. Regulation of the Escherichia coli hfq gene encoding the host factor for phage Q beta. J. Bacteriol. 176:531-534.
30. Kaldalu, N., R. Mei, and K. Lewis. 2004. Killing by ampicillin and ofloxacin induces overlapping changes in Escherichia coli transcription profile. Antimicrob. Agents Chemother. 48:890-896.
31. Kihara, A., Y. Akiyama, and K. Ito. 1996. A protease complex in the Escherichia coli plasma membrane: HflKC (HflA) forms a complex with FtsH (HflB), regulating its proteolytic activity against SecY. EMBO J. 15:6122- 6131.
32. Kihara, A., Y. Akiyama, and K. Ito. 1997. Host regulation of lysogenic decision in bacteriophage -: transmembrane modulation of FtsH (HflB), the cII degrading protease, by HflKC (HflA). Proc. Natl. Acad. Sci. USA 94: 5544-5549.
33. Kihara, A., Y. Akiyama, and K. Ito. 2001. Revisiting the lysogenisation control of bacteriophage -. Identification and characterization of a new host component, HflD. J. Biol. Chem. 276:13695-13700.
34. Klinger, C., M. Rossbach, R. Howe, and M. Kaufmann. 2003. Thermophile- specific proteins: the gene product of aq-1292 from Aquifex aeolicus is an NTPase. BMC Biochem. 4:12.
35. Koonin, E. V., Y. I. Wolf, and L. Arvind. 2000. Protein fold recognition using sequence profiles and its application in structural genomics. Adv. Protein Chem. 54:245-275.
36. Leipe, D. D., Y. I. Wolf, E. V. Koonin, and L. Arvind. 2002. Classification and evolution of P-loop GTPases and related ATPases. J. Mol. Biol. 317:41-72.
37. Lieb, M., and S. Rehmat. 1995. Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins. J. Bacteriol. 177:660- 666.
38. Mayer, M. P. 1995. A new set of useful cloning expression vectors derived from pBlueScript. Gene 163:41-46.
39. McGuffin, L. J., K. Bryson, and D. T. Jones. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16:404-405.
40. Mellon, I., and G. Champe. 1996. Products of DNA mismatch repair genes mutS and mutL are required for transcription-coupled nucleotide-excision repair of the lactose operon in Escherichia coli. Natl. Acad. Sci. USA 93: 1292-1297.
41. Modrich, P. 1995. Mismatch repair, genetic stability and tumour avoidance. Phil. Trans. R. Soc. Lond. B 347:89-95.
42. Noble, J. A., M. A. Innis, E. V. Koonin, K. E. Rudd, F. Banuett, and I. Herskowitz. 1993. The Escherichia coli hflA locus encodes a putative GTPbinding protein and two membrane proteins, one of which contains a protease- like domain. Proc. Natl. Acad. Sci. USA 90:10866-10870.
43. Ouali, M., and R. D. King. 2000. Cascaded multiple classifiers for secondary strucure prediction. Protein Sci. 9:1162-1176.
44. Polkinghorne, A., U. Ziegler, Y. Gonzalez-Hernandez, A. Pospischil, P. Timms, and L. Vaughan. 2008. Chlamydophila pneumoniae HflX belongs to an uncharacterized family of conserved GTPases and associates with the Escherichia coli 50S large ribosomal subunit. Microbiology 154:3537-3546.
45. Richmond, C. S., J. D. Glasner, R. Mau, H. Jin, and F. R. Blattner. 1999. Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res. 27:3821-3835.
46. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed., p. A.1-A.2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
47. Sazuka, T., Y. Tomooka, Y. Ikawa, M. Noda, and S. Kumar. 1992. Drg: a novel developmentally regulated GTP-binding protein. Biochem. Biophys. Res. Commun. 189:363-370.
48. Shotland, Y., S. Koby, D. Teff, N. Mansur, D. A. Oren, K. Tatematsu, T. Tomoyasu, M. Kessel, B. Bukau, T. Ogura, and A. B. Oppenheim. 1997. Proteolysis of the phage lambda CII regulatory protein by FtsH (HflB) of Escherichia coli. Mol. Microbiol. 24:1303-1310.
49. Swingle, B., M. O'Carroll, D. Haniford, and K. M. Derbyshire. 2004. The effect of host-encoded nucleoid proteins on transposition: H-NS influences targeting of both IS903 and Tn10. Mol. Microbiol. 52:1055-1067.
50. Tomoyasu, T., K. Yamanaka, K. Murata, T. Suzaki, P. Bouloc, A. Kato, H. Niki, S. Hiraga, and T. Ogura. 1993. Topology and subcellular localization of FtsH protein in Escherichia coli. J. Bacteriol. 175:1352-1357.
51. Tomoyasu, T., T. Yuki, S. Morimura, H. Mori, K. Yamanaka, H. Niki, S. Hiraga, and T. Ogura. 1993. The Escherichia coli FtsH protein is a prokaryotic member of a protein family of putative ATPases involved in membrane functions, cell cycle control, and gene expression. J. Bacteriol. 175:1344- 1351.
52. Tsui, H. C., G. Feng, and M. E. Winkler. 1996. Transcription of the mutL repair, miaA tRNA modification, hfq pleiotropic regulator, and hflA region protease genes of Escherichia coli K-12 from clustered E-32-specific promoters during heat shock. J. Bacteriol. 178:5719-5731.
53. Tsui, H. C., H. C. Leung, and M. E. Winkler. 1994. Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Mol. Microbiol. 13:35-49.
54. Twiss, E., A. M. Coros, N. P. Tavakoli, and K. M. Derbyshire. 2005. Transposition is modulated by a diverse set of host factors in Escherichia coli and is stimulated by nutritional stress. Mol. Microbiol. 57:1593-1607.
55. Weber, A., A. S. Kogl, and K. Jung. 2006. Time-dependent proteome alterations under osmotic stress during aerobic and anaerobic growth in Escherichia coli. J. Bacteriol. 188:7165-7175.
56. Wegrzyn, G., and A. Wegrzyn. 2005. Genetic switches during bacteriophage λ development. Prog. Nucleic Acid Res. Mol. Biol. 7:1-48.