Global transcriptome analysis of the E. coli O157 response to Agrimonia pilosa extract

Molecular and Cellular Toxicology

Volumn 7, Issue 3, 2011, Pages 299-310

  Yang, Hea Jung ^a   Jung, Yune Suk ^a   Kim, Ki Suk ^a   Choi, Eun Kyeong ^a   Lim, Dong Jin ^a   Ahn, Kwang Seok ^a   Jung, Hee Jae ^a   Jung, Sung Ki ^a   Jang, Hyeung Jin ^a  

^a Kyung Hee University   (South Korea)

Author keywords

Agrimonia pilosa; Antibiotic; Cell wall inhibition; Cys sulfur metabolism; FolA

Indexed keywords

EID: 84863011514     PISSN: 1738642X     EISSN: 20928467     Source Type: Journal    
DOI: 10.1007/s13273-011-0036-7     Document Type: Article

References (70)

1. Chen, Y., Guo, J. J., Healy, D. P., Lin, X. & Patel, N. C. Risk of hepatotoxicity associated with the use of telithromycin: a signal detection using data mining algorithms. Ann Pharmacother 42:1791-1796 (2008).
2. Waksman, S. A. What is an antibiotic or an antibiotic substance. Micologia 5:565-569 (1947).
3. Lee, Y. H., Kim, M. B. & Chung, D. S. Effect of extract Agrimonia pilosa L. on biological activity in rats Korean. J Medicinal Crop Sci 10:167 (2002).
4. Correia, H., Gonzalez-Paramas, A., Amaral, M. T., Santos-Buelga, C. & Batista, M. T. Polyphenolic profile characterization of Agrimonia eupatoria L. by HPLC with different detection devices. Biomed Chromatogr 20:88-94 (2006). (Pubitemid 43141410)
5. Copland, A. et al. Antibacterial and free radical scavenging activity of the seeds of Agrimonia eupatoria. Fitoterapia 74:133-135 (2003). (Pubitemid 36287259)
6. Pichler, W. J., Daubner, B. & Kawabata, T. Drug hypersensitivity: Flare-up reactions, cross-reactivity and multiple drug hypersensitivity. J Dermatol 38:216-221 (2011).
7. Lescop, E. et al. The solution structure of Escherichia coli Wzb reveals a novel substrate recognition mechanism of prokaryotic low molecular weight proteintyrosine phosphatases. J Biol Chem 281:19570-19577 (2006). (Pubitemid 44035460)
8. Chiarugi, P. et al. The Src and signal transducers and activators of transcription pathways as specific targets for low molecular weight phosphotyrosine-protein phosphatase in platelet-derived growth factor signaling. J Biol Chem 273:6776-6785 (1998). (Pubitemid 28160340)
9. Stein, E. et al. Eph receptors discriminate specific lig-and oligomers to determine alternative signaling complexes, attachment, and assembly responses. Genes Dev 12:667-678 (1998). (Pubitemid 28134299)
10. Ramponi, G. & Stefani, M. Structure and function of the low Mr phosphotyrosine protein phosphatases. Biochim Biophys Acta 1341:137-156 (1997). (Pubitemid 27451930)
11. al-Bar, O. A., O'Connor, C. D., Giles, I. G. & Akhtar, M. D-alanine: D-alanine ligase of Escherichia coli. Expression, purification and inhibitory studies on the cloned enzyme. Biochem J 282:747-752 (1992).
12. Defeu Soufo, H. J. et al. Bacterial translation elongation factor EF-Tu interacts and colocalizes with actin-like MreB protein. Proc Natl Acad Sci USA 107:3163-3168 (2010).
13. Kawai, Y., Daniel, R. A. & Errington, J. Regulation of cell wall morphogenesis in Bacillus subtilis by recruitment of PBP1 to the MreB helix. Mol Microbiol 71: 1131-1144 (2009).
14. Meisel, U., Holtje, J. V. & Vollmer, W. Overproduction of inactive variants of the murein synthase PBP1B causes lysis in Escherichia coli. J Bacteriol 185:5342-5348 (2003). (Pubitemid 37082390)
15. Magnet, S. et al. Identification of the L,D-transpeptidases responsible for attachment of the Braun lipoprotein to Escherichia coli peptidoglycan. J Bacteriol 189: 3927-3931 (2007). (Pubitemid 46740192)
16. Kiino, D. R., Singer, M. S. & Rothman-Denes, L. B. Two overlapping genes encoding membrane proteins required for bacteriophage N4 adsorption. J Bacteriol 175:7081-7085 (1993). (Pubitemid 23322461)
17. Bleuel, C. et al. TolC is involved in enterobactin efflux across the outer membrane of Escherichia coli. J Bacteriol 187:6701-6707 (2005). (Pubitemid 41356243)
18. Meng, Y. L., Liu, Z. & Rosen, B. P. As(III) and Sb(III) uptake by GlpF and efflux by ArsB in Escherichia coli. J Biol Chem 279:18334-18341 (2004). (Pubitemid 38623248)
19. Prakash, S., Cooper, G., Singhi, S. & Saier, M. H., Jr. The ion transporter superfamily. Biochim Biophys Acta 1618:79-92 (2003). (Pubitemid 37487842)
20. Rabus, R., Jack, D. L., Kelly, D. J. & Saier, M. H., Jr. TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters. Microbiology 145:3431-3445 (1999). (Pubitemid 30018787)
21. Higashi, K. et al. Identification of a spermidine excretion protein complex (MdtJI) in Escherichia coli. J Bacteriol 190:872-878 (2008). (Pubitemid 351170930)
22. Soskine, M., Mark, S., Tayer, N., Mizrachi, R. & Schuldiner, S. On parallel and antiparallel topology of a homodimeric multidrug transporter. J Biol Chem 281: 36205-36212 (2006). (Pubitemid 46041355)
23. Kashiwagi, K. et al. Identification of the putrescine recognition site on polyamine transport protein PotE. J Biol Chem 275:36007-36012 (2000).
24. Soksawatmaekhin, W., Uemura, T., Fukiwake, N., Kashiwagi, K. & Igarashi, K. Identification of the cadaverine recognition site on the cadaverine-lysine antiporter CadB. J Biol Chem 281:29213-29220 (2006). (Pubitemid 44507064)
25. Nagakubo, S., Nishino, K., Hirata, T. & Yamaguchi, A. The putative response regulator BaeR stimulates multidrug resistance of Escherichia coli via a novel multidrug exporter system, MdtABC. J Bacteriol 184: 4161-4167 (2002). (Pubitemid 34774296)
26. Nishino, K. & Yamaguchi, A. EvgA of the two-component signal transduction system modulates production of the yhiUV multidrug transporter in Escherichia coli. J Bacteriol 184:2319-2323 (2002). (Pubitemid 34259685)
27. Adnan, M., Morton, G., Singh, J. & Hadi, S. Contribution of rpoS and bolA genes in biofilm formation in Escherichia coli K-12 MG1655. Mol Cell Biochem 342:207-213 (2010).
28. Ito, A., May, T., Taniuchi, A., Kawata, K. & Okabe, S. Localized expression profiles of rpoS in Escherichia coli biofilms. Biotechnol Bioeng 103:975-983 (2009).
29. Rahman, M., Hasan, M. R., Oba, T. & Shimizu, K. Effect of rpoS gene knockout on the metabolism of Escherichia coli during exponential growth phase and early stationary phase based on gene expressions, enzyme activities and intracellular metabolite concentrations. Biotechnol Bioeng 94:585-595 (2006).
30. Saint-Ruf, C., Taddei, F. & Matic, I. Stress and survival of aging Escherichia coli rpoS colonies. Genetics 168:541-546 (2004). (Pubitemid 39346615)
31. Griffith, K. L. & Wolf, R. E., Jr. Genetic evidence for pre-recruitment as the mechanism of transcription activation by SoxS of Escherichia coli: the dominance of DNA binding mutations of SoxS. J Mol Biol 344: 1-10 (2004). (Pubitemid 39422371)
32. Zafar, M. A., Shah, I. M. & Wolf, R. E., Jr. Proteinprotein interactions between sigma(70) region 4 of RNA polymerase and Escherichia coli SoxS, a transcription activator that functions by the prerecruitment mechanism: evidence for "off-DNA" and "on-DNA" interactions. J Mol Biol 401:13-32 (2010).
33. Shah, I. M. & Wolf, R. E., Jr. Novel protein - protein interaction between Escherichia coli SoxS and the DNA binding determinant of the RNA polymerase alpha subunit: SoxS functions as a co-sigma factor and redeploys RNA polymerase from UP-element-containing promoters to SoxS-dependent promoters during oxidative stress. J Mol Biol 343:513-532 (2004). (Pubitemid 39311602)
34. Pinto, R., Tang, Q. X., Britton, W. J., Leyh, T. S. & Triccas, J. A. The Mycobacterium tuberculosis cysD and cysNC genes form a stress-induced operon that encodes a tri-functional sulfate-activating complex. Microbiology 150:1681-1686 (2004). (Pubitemid 38923667)
35. Rudolph, C. J., Upton, A. L., Briggs, G. S. & Lloyd, R. G. Is RecG a general guardian of the bacterial genome? DNA Repair (Amst) 9:210-223 (2010).
36. Bohr, V. A. Rising from the RecQ-age: the role of human RecQ helicases in genome maintenance. Trends Biochem Sci 33:609-620 (2008).
37. Scrima, A., Vetter, I. R., Armengod, M. E. & Wittinghofer, A. The structure of the TrmE GTP-binding protein and its implications for tRNA modification. EMBO J 24:23-33 (2005). (Pubitemid 40188460)
38. Bohme, S. et al. Stabilization of G domain conformations in the tRNA-modifying MnmE-GidA complex observed with double electron electron resonance spectroscopy. J Biol Chem 285:16991-17000 (2010).
39. Nakayama, N., Bond, M. W., Miyajima, A., Kobori, J. & Arai, K. Structure of Escherichia coli dnaC. Identification of a cysteine residue possibly involved in association with dnaB protein. J Biol Chem 262:10475-10480 (1987).
40. Shao, Y., Feldman-Cohen, L. S. & Osuna, R. Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site. J Mol Biol 380:327-339 (2008).
41. Kamen, B. Folate and antifolate pharmacology. Semin Oncol 24:S18-30-S18-39 (1997).
42. Fenech, M., Aitken, C. & Rinaldi, J. Folate, vitamin B12, homocysteine status and DNA damage in young Australian adults. Carcinogenesis 19:1163-1171 (1998). (Pubitemid 28375365)
43. Zittoun, J. Anemias due to disorder of folate, vitamin B12 and transcobalamin metabolism. Rev Prat 43:1358-1363 (1993).
44. Smith, J. M. & Daum, H. A., 3rd Identification and nucleotide sequence of a gene encoding 5'-phosphori-bosylglycinamide transformylase in Escherichia coli K12. J Biol Chem 262:10565-10569 (1987).
45. Hondorp, E. R. & Matthews, R. G. Oxidation of cysteine 645 of cobalamin-independent methionine synthase causes a methionine limitation in Escherichia coli. J Bacteriol 191:3407-3410 (2009).
46. Gon, S., Jourlin-Castelli, C., Theraulaz, L. & Mejean, V. An unsuspected autoregulatory pathway involving apocytochrome TorC and sensor TorS in Escherichia coli. Proc Natl Acad Sci USA 98:11615-11620 (2001). (Pubitemid 32928777)
47. Ansaldi, M., Bordi, C., Lepelletier, M. & Mejean, V. TorC apocytochrome negatively autoregulates the trimethylamine N-oxide (TMAO) reductase operon in Escherichia coli. Mol Microbiol 33:284-295 (1999). (Pubitemid 29322515)
48. Gon, S., Giudici-Orticoni, M. T., Mejean, V. & Iobbi-Nivol, C. Electron transfer and binding of the c-type cytochrome TorC to the trimethylamine N-oxide reductase in Escherichia coli. J Biol Chem 276:11545-11551 (2001).
49. Genest, O., Ilbert, M., Mejean, V. & Iobbi-Nivol, C. TorD, an essential chaperone for TorA molybdoenzyme maturation at high temperature. J Biol Chem 280: 15644-15648 (2005). (Pubitemid 40616682)
50. Ilbert, M., Mejean, V., Giudici-Orticoni, M. T., Samama, J. P. & Iobbi-Nivol, C. Involvement of a mate chaperone (TorD) in the maturation pathway of molybdoenzyme TorA. J Biol Chem 278:28787-28792 (2003). (Pubitemid 36935788)
51. Guymer, D., Maillard, J., Agacan, M. F., Brearley, C. A. & Sargent, F. Intrinsic GTPase activity of a bacterial twin-arginine translocation proofreading chaperone induced by domain swapping. FEBS J 277:511-525 (2010).
52. Young, J. C. Mechanisms of the Hsp70 chaperone system. Biochem Cell Biol 88:291-300 (2010).
53. Chang, L., Thompson, A. D., Ung, P., Carlson, H. A. & Gestwicki, J. E. Mutagenesis reveals the complex relationships between ATPase rate and the chaperone activities of Escherichia coli heat shock protein 70 (Hsp70/DnaK). J Biol Chem 285:21282-21291 (2010).
54. Sugimoto, S., Saruwatari, K., Higashi, C. & Sonomoto, K. The proper ratio of GrpE to DnaK is important for protein quality control by the DnaK-DnaJ-GrpE chaperone system and for cell division. Microbiology 154: 1876-1885 (2008).
55. Tapley, T. L., Cupp-Vickery, J. R. & Vickery, L. E. Structural determinants of HscA peptide-binding specificity. Biochemistry 45:8058-8066 (2006). (Pubitemid 43993226)
56. Aoto, P. C., Ta, D. T., Cupp-Vickery, J. R. & Vickery, L. E. X-ray diffraction analysis of a crystal of HscA from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 61:715-717 (2005). (Pubitemid 44210837)
57. Hennessy, F., Nicoll, W. S., Zimmermann, R., Cheetham, M. E. & Blatch, G. L. Not all J domains are created equal: implications for the specificity of Hsp40-Hsp70 interactions. Protein Sci 14:1697-1709 (2005). (Pubitemid 41001413)
58. Koike-Takeshita, A., Yoshida, M. & Taguchi, H. Revisiting the GroEL-GroES reaction cycle via the symmetric intermediate implied by novel aspects of the GroEL(D398A) mutant. J Biol Chem 283:23774-23781 (2008).
59. Weissman, J. S. et al. Mechanism of GroEL action: productive release of polypeptide from a sequestered position under GroES. Cell 83:577-587 (1995).
60. Chaudhuri, T. K., Verma, V. K. & Maheshwari, A. GroEL assisted folding of large polypeptide substrates in Escherichia coli: Present scenario and assignments for the future. Prog Biophys Mol Biol 99:42-50 (2009).
61. Carrio, M. M. & Villaverde, A. Localization of chaperones DnaK and GroEL in bacterial inclusion bodies. J Bacteriol 187:3599-3601 (2005). (Pubitemid 40628721)
62. Fredriksson, A., Ballesteros, M., Dukan, S. & Nystrom, T. Defense against protein carbonylation by DnaK/DnaJ and proteases of the heat shock regulon. J Bacteriol 187:4207-4213 (2005). (Pubitemid 40827802)
63. Kuczynska-Wisnik, D., Matuszewska, E. & Laskowska, E. Escherichia coli heat-shock proteins IbpA and IbpB affect biofilm formation by influencing the level of extracellular indole. Microbiology 156:148-157 (2009).
64. Ratajczak, E., Zietkiewicz, S. & Liberek, K. Distinct activities of Escherichia coli small heat shock proteins IbpA and IbpB promote efficient protein disaggregation. J Mol Biol 386:178-189 (2009).
65. Gaubig, L. C., Waldminghaus, T. & Narberhaus, F. Multiple layers of control govern expression of the Escherichia coli ibpAB heat-shock operon. Microbiology 157:66-76 (2010).
66. Bissonnette, S. A., Rivera-Rivera, I., Sauer, R. T. & Baker, T. A. The IbpA and IbpB small heat-shock proteins are substrates of the AAA+ Lon protease. Mol Microbiol 75:1539-1549 (2010).
67. Leyh, T. S., Vogt, T. F. & Suo, Y. The DNA sequence of the sulfate activation locus from Escherichia coli K-12. J Biol Chem 267:10405-10410 (1992).
68. Berendt, U., Haverkamp, T., Prior, A. & Schwenn, J. D. Reaction mechanism of thioredoxin: 3'-phosphoadenylylsulfate reductase investigated by site-directed mutagenesis. Eur J Biochem 233:347-356 (1995).
69. Matijasevic, Z., Hajec, L. I. & Volkert, M. R. Anaerobic induction of the alkylation-inducible Escherichia coli aidB gene involves genes of the cysteine biosyn-thetic pathway. J Bacteriol 174:2043-2046 (1992).
70. Ostrowski, J. et al. Characterization of the cysJIH regions of Salmonella typhimurium and Escherichia coli B. DNA sequences of cysI and cysH and a model for the siroheme-Fe4S4 active center of sulfite reductase hemoprotein based on amino acid homology with spinach nitrite reductase. J Biol Chem 264:15726-15737 (1989). (Pubitemid 19242953)