Cell response of Escherichia coli to cisplatin-induced stress

Proteomics

Volumn 11, Issue 21, 2011, Pages 4174-4188

  Stefanopoulou, Maria ^a   Kokoschka, Malte ^a   Sheldrick, William S ^a   Wolters, Dirk A ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

Cisplatin; Cytostatic cell response; Escherichia coli; Microbiology

Indexed keywords

ACONITATE HYDRATASE 2; ACONITIC ACID; AMINO ACID; CHAPERONIN; CHAPERONIN 1; CISPLATIN; ENOLASE; HYDROLYASE; NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHATASE; NUCLEOTIDE PYROPHOSPHATASE; RIBOSOME PROTEIN; RIBOSOME PROTEIN S1; UNCLASSIFIED DRUG; ANTINEOPLASTIC AGENT; ESCHERICHIA COLI PROTEIN; INORGANIC PYROPHOSPHATASE; MAZG PROTEIN, E COLI;

AMINO ACID SEQUENCE; APOPTOSIS; ARTICLE; CATABOLISM; CELL STRESS; ENERGY METABOLISM; ESCHERICHIA COLI; GENE REGULATORY NETWORK; GLYCOLYSIS; LIQUID CHROMATOGRAPHY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN SYNTHESIS; RIBOSOME SUBUNIT; TANDEM MASS SPECTROMETRY; CHEMICAL STRUCTURE; CHEMISTRY; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS;

ESCHERICHIA COLI;

AMINO ACID SEQUENCE; ANTINEOPLASTIC AGENTS; CISPLATIN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PYROPHOSPHATASES;

EID: 84856601917     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100203     Document Type: Article

References (96)

1. Rosenberg, B., van Camp, L., Krigas, T., Inhibition of cell division in Escherichia coli by electrolysis products from a platinum electrode. Nature 1965, 205, 698-699.
2. Rosenberg, B., van Camp, L., Trosko, J. E., Mansour, V. H., Platinum compounds: a new class of potent antitumour agents. Nature 1969, 222, 385-386.
3. 2. J. Am. Chem. Soc. 1982, 104, 5793-5795.
4. Fichtinger-Schepman, A. M., Van der Veer, J. L., Den Hartog, J. H., Lohman, P. H., Reedijk, J., Adducts of the antitumor drug cis-diamminedichloroplatinum(II) with DNA: formation, identification, and quantitation. Biochemistry 1985, 24, 707-713.
5. Eastman, A., Reevaluation of interaction of cis-dichloro(ethylenediamine)platinum(II) with DNA. Biochemistry 1986, 25, 3912-3915.
6. Terheggen, P. M. A. B., Floot, B. G. J., Scherer, E., Begg, A. C. et al., Immunocytochemical detection of interaction products of cis-diamminedichloroplatinum(II) and cis-diammine(1,1-cyclobutanedicarboxylato)platinum(II) with DNA in rodent tissue sections. Cancer Res. 1987, 47, 6719-6725.
7. Takahara, P. M., Rosenzweig, A. C., Frederick, C. A., Lippard, S. J., Crystal structure of double-stranded DNA containing the major adduct of the anticancer drug cisplatin. Nature 1995, 377, 649-652.
8. Takahara, P. M., Frederick, C. A., Lippard, S. J., Crystal structure of the anticancer drug cisplatin bound to duplex DNA. J. Am. Chem. Soc. 1996, 118, 12309-12321.
9. Marzilli, L. G., Saad, J. S., Kuklenyik, Z., Keating, K. A., Xu, Y., Relationship of solution and protein-bound structures of DNA duplexes with the major intrastrand cross-link lesions formed on cisplatin binding to DNA. J. Am. Chem. Soc. 2001, 123, 2764-2770.
10. Sullivan, S. T., Saad, . S., Fanizzi, F. P., Marzilli, L. G., Dramatic 50'-residue effect on conformer distribution of short oligonucleotide retro models of the cisplatinDNA cross-link: implications for the lippard and cross-link distorted base pair steps present in cisplatinDNA duplex adducts. J. Am. Chem. Soc. 2002, 124, 1558-1559.
11. Todd, R. C., Lippard, S. J., Inhibition of transcription by platinum antitumor compounds. Metallomics 2009, 1, 280-291.
12. Wang, D., Lippard, S. J., Cellular processing of platinum anticancer drugs. Nat. Rev. Drug Discov. 2005, 4, 307-320.
13. Baselga, J., Arteaga, C. L., Critical update and emerging trends in epidermal growth factor receptor targeting in cancer. J. Clin. Oncol. 2005, 23, 2445-2459.
14. Jain, R. K., Duda, D. G., Clark, J. W., Loeffler, J. S., Lessons from phase III clinical trials on anti-VEGF therapy for cancer. Nat. Clin. Pract. Oncol. 2006, 3, 24-40.
15. Casini, A., Gabbiani, C., Sorrentino, F., Rigobello, M. P. et al., Emerging protein targets for anticancer metallodrugs: inhibition of thioredoxin reductase and cathepsin B by antitumor ruthenium(II)-arene compounds. J. Med. Chem. 2008, 51, 6773-6781.
16. Tonella, L., Hoogland, C., Binz, P. A., Appel, R. D. et al., New perspectives in the Escherichia coli proteome investigation. Proteomics 2001, 1, 409-423.
17. Corbin, R. W., Paliy, O., Yang, F., Shabanowitz, J. et al., Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc. Natl. Acad. Sci. USA 2003, 100, 9232-9237.
18. Jensen, P. K., Pasa-Tolić, L., Anderson, G. A., Horner, J. A. et al., Probing proteomes using capillary isoelectric focusing-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 1999, 71, 2076-2084.
19. Jensen, P. K., Pasa-Tolić, L., Peden, K. K., Martinović, S. et al., Mass spectrometric detection for capillary isoelectric focusing separations of complex protein mixtures. Electrophoresis 2000, 21, 1372-1380.
20. Iwasaki, M., Miwa, S., Ikegami, T., Tomita, M. et al., One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. Anal. Chem. 2010, 82, 2616-2620.
21. Blattner, F. R., Plunkett, G., 3rd, Bloch, C. A., Perna, N. T. et al., The complete genome sequence of Escherichia coli K-12. Science 1997, 277, 1453-1462.
22. Will, J., Sheldrick, W. S., Wolters, D., Characterisation of cisplatin coordination sites in cellular Escherichia coli DNA-binding proteins by combined biphasic liquid chromatography and ESI tandem mass spectrometry. J. Biol. Inorg. Chem. 2008, 13, 421-434.
23. Esteban-Fernández, D., Moreno-Gordaliza, E., Cañas, B., Palacios, M. A., Gómez-Gómez, M. M., Analytical methodologies for metallomics studies of antitumor Pt-containing drugs. Metallomics 2010, 2, 19-38.
24. Wilson, L. A., Yamamoto, H., Singh, G., Role of the transcription factor Ets-1 in cisplatin resistance. Mol. Cancer Ther. 2004, 3, 823-832.
25. Voortman, J., Checinska, A., Giaccone, G., Rodriguez, J. A., Kruyt, F. A., Bortezomib, but not cisplatin, induces mitochondria-dependent apoptosis accompanied by up-regulation of noxa in the non-small cell lung cancer cell line NCI-H460. Mol. Cancer Ther. 2007, 6, 1046-1053.
26. Stevens, E. V., Nishizuka, S., Antony, S., Reimers, M. et al., Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers. Mol. Cancer Ther. 2008, 7, 10-18.
27. Zhang, L., Zheng, Y., Callahan, B., Belfort, M. et al., Cisplatin inhibits protein splicing, suggesting inteins as therapeutic targets in mycobacteria. J. Biol. Chem. 2011, 286, 1277-1282.
28. Mitchison, D. A., Drug resistance in tuberculosis. Eur. Respir. J. 2005, 25, 376-379.
29. Liu, H., Sadygov, R. G., Yates, . R., 3rd, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem. 2004, 76, 4193-4201.
30. Fränzel, B., Trötschel, C., R. uckert, C., Kalinowski, J. et al., Adaptation of Corynebacterium glutamicum to salt-stress conditions. Proteomics 2010, 10, 445-457.
31. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G. et al., The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
32. Guex, N., Peitsch, M. C., SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997, 18, 2714-2723.
33. Arnold, K., Bordoli, L., Kopp, J., Schwede, T., The SWISS-MODEL Workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006, 22, 195-201.
34. Kiefer, F., Arnold, K., K.ünzli, M., Bordoli, L., Schwede, T., The SWISS-MODEL Repository and associated resources. Nucleic Acids Res. 2009, 37, D387-D392.
35. Schwede, T., Kopp, J., Guex, N., Peitsch, M. C., SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 2003, 31, 3381-3385.
36. Rappé, A. K., Casewit, C. J., Colwell, K. S., Goddard, W. A., Skiff, W.M., UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 1992, 114, 10024-10035.
37. Casewit, C. J., Colwell, K. S., Rappé, A. K., Application of a universal force field to organic molecules. J. Am. Chem. Soc. 1992, 114, 10035-10046.
38. Rappé, A. K., Colwell, K. S., Casewit, C. J., Application of a universal force field to metal complexes. Inorg. Chem. 1993, 32, 3438-3450.
39. Becke, A. D., Density-functional thermochemistry III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648-5652.
40. Lee, C., Yang, W., Parr, R. G., Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 1998, 37, 785-789.
41. Vosko, S. H., Wilk, L., Nusair, M., Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis. Can. J. Phys. 1980, 58, 1200-1211.
42. Stephens, P. J., Devlin, F. J., Chabalowski, C. F., Frisch, M. J., Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem. 1994, 98, 11623-11627.
43. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E. et al., Gaussian 09, Revision A.2. Gaussian Inc. 2009, Wallingford CT, USA.
44. Weigend, F., Ahlrichs, R., Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: design and assessment of accuracy. Phys. Chem. Chem. Phys. 2005, 7, 3297-3305.
45. Feller, D., The role of databases in support of computational chemistry calculations. J. Comp. Chem. 1996, 17, 1571-1586.
46. Schuchardt, K. L., Didier, B. T., Elsethagen, T., Sun, L. et al., Basis set exchange: a community database for computational sciences. J. Chem. Inf. Model. 2007, 47, 1045-1052.
47. Miertuš, S., Scrocco, E., Tomasi, J., Electrostatic interaction of a solute with a continuum. a direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chem. Phys. 1981, 55, 117-129.
48. Gruer, M. J., Guest, J. R., Two genetically-distinct and differentially-regulated aconitases (AcnA and AcnB) in Escherichia coli. Microbiology 1994, 140, 2531-2541.
49. Bradbury, A. J., Gruer, M. J., Rudd, K. E., Guest, J. R., The second aconitase (AcnB) of Escherichia coli. Microbiology 1996, 142, 389-400.
50. Nöllmann, M., Crisona, N. J., Arimondo, P. B., Thirty years of Escherichia coli DNA gyrase: from in vivo function to single-molecule mechanism. Biochimie 2007, 89, 490-499.
51. Bordes, P., Conter, A., Morales, V., Bouvier, J. et al., DNA supercoiling contributes to disconnect sigmaS accumulation from sigmaS-dependent transcription in Escherichia coli. Mol. Microbiol. 2003, 48, 561-571.
52. Higgins, C. F., Dorman, C. J., Stirling, D. A., Waddell, L. et al., A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. Typhimurium and E. coli. Cell 1988, 52, 569-584.
53. Dorman, C. J., Barr, G. C., Nỳý Bhriain, N., Higgins, C. F., DNA supercoiling and the anaerobic and growth phase regulation of tonB gene expression. J. Bacteriol. 1988, 170, 2816-2826.
54. Yamamoto, N., Droffner, M. L., Mechanisms determining aerobic or anaerobic growth in the facultative anaerobe Salmonella typhimurium. Proc. Natl. Acad. Sci. USA 1985, 82, 2077-2081.
55. Hsieh, L. S., Burger, R. M., Drlica, K., Bacterial DNA super-coiling and [ATP]/[ADP]. Changes associated with a transition to anaerobic growth. J. Mol. Biol. 1991, 19, 443-450.
56. Hsieh, L. S., Rouvie're-Yaniv, J., Drlica, K., Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock. J. Bacteriol. 1991, 173, 3914-3917.
57. Huo, Y. X., Rosenthal, A. Z., Gralla, J. D., General stress response signalling: unwrapping transcription complexes by DNA relaxation via the sigma38 C-terminal domain. Mol. Microbiol. 2008, 70, 369-378.
58. Mojica, F. J., Charbonnier, F., Juez, G., Rodrỳýguez-Valera, F., Forterre, P., Effects of salt and temperature on plasmid topology in the halophilic archaeon Haloferax volcanii. J. Bacteriol. 1994, 176, 4966-4973.
59. Bagramyan, K., Trchounian, A., Structural and functional features of formate hydrogen lyase, an enzyme of mixed-acid fermentation from Escherichia coli. Biochemistry (Moscow) 2003, 68, 1159-1170.
60. Hayes, E. T., Wilks, J. C., Sanfilippo, P., Yohannes, E. et al., Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12. BMC Microbiol. 2006, 6, 89.
61. Lutz, S., Jacobi, A., Schlensog, V., Böhm, R. et al., Molecular characterization of an operon (hyp) necessary for the activity of the three hydrogenase isoenzymes in Escherichia coli. Mol. Microbiol. 1991, 5, 123-135.
62. Yoshida, A., Nishimura,T., Kawaguchi, H., Inui, M., Yukawa, H., Enhanced hydrogen production from formic acid by formate hydrogen lyase-overexpressing Escherichia coli strains. Appl. Environ. Microbiol. 2005, 71, 6762-6768.
63. Ogawa, H., Gomi, T., Fujioka, M., Serine hydro-xymethyltransferase and threonine aldolase: are they identical? Int. J. Biochem. Cell Biol. 2000, 32, 289-301.
64. Agrawal, S., Kumar, A., Srivastava, V., Mishra, B. N., Cloning, expression, activity and folding studies of serine hydroxymethyltransferase: a target enzyme for cancer chemotherapy. J. Mol. Microbiol. Biotechnol. 2003, 6, 67-75.
65. Park, S. J., Cotter, P. A., Gunsalus, R. P., Regulation of malate dehydrogenase (mdh) gene expression in Escherichia coli in response to oxygen, carbon, and heme availability. J. Bacteriol. 1995, 177, 6652-6656.
66. Morita, T., Maki, K., Aiba, H., RNase E-based ribonucleo-protein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Gene Dev. 2005, 19, 2176-2186.
67. Khemici, V., Toesca, I., Poljak, L., Vanzo, N. F., Carpousis, A. J., The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: functional replacement of RhlB by RhlE. Mol. Microbiol. 2004, 54, 1422-1430.
68. Prud'homme-Genereux, A., Beran, R. K., Iost, I., Ramey, C. S. et al., Physical and functional interactions among RNase E, polynucleotide phosphorylase and the coldshock protein, CsdA: evidence for a 'cold shock degradosome'. Mol. Microbiol. 2004, 54, 1409-1421.
69. Zhang, S., Barr, B. K., Wilson, D. B., Effects of noncatalytic residue mutations on substrate specificity and ligand binding of Thermobifida fusca endocellulase cel6A. Eur. J. Biochem. 2000, 267, 244-252.
70. Minasov, G., Padavattan, S., Shuvalova, L., Brunzelle, J. S. et al., Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains. J. Biol. Chem. 2009, 284, 13174-13184.
71. Sørensen, M. A., Fricke, J., Pedersen, S., Ribosomal protein S1 is required for translation of most, if not all, natural mRNAs in Escherichia coli in vivo. J. Mol. Biol. 1998, 280, 561-569.
72. Paul, B., Barker, M., Ross, W., Schneider, D. et al., DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 2004, 118, 311-322.
73. Paul, B., Berkmen, M., Gourse, R., DksA potentiates direct activation of amino acid promoters by ppGpp. Proc. Natl. Acad. Sci. USA 2005, 102, 7823-7828.
74. Weijland, A., Harmark, K., Cool, R. H., Anborgh, P. H., Parmeggiani, A., Elongation factor Tu: a molecular switch in protein biosynthesis. Mol. Microbiol. 1992, 6, 683-688.
75. Baneyx, F., Nannenga, B. L., Chaperones: a story of thrift unfolds. Nat. Chem. Biol. 2010, 6, 880-881.
76. Slepenkov, S. V., Witt, S. N., The unfolding story of the Escherichia coli Hsp70 DnaK: is DnaK a holdase or an unfoldase? Mol. Microbiol. 2002, 45, 1197-1206.
77. Gross, M., Marianovsky, I., Glaser, G., MazG-a regulator of programmed cell death in Escherichia coli. Mol. Microbiol. 2006, 59, 590-601.
78. Aizenman, E., Engelberg-Kulka, H., Glaser, G., An Escherichia coli chromosomal 'addiction module' regulated by guanosine [corrected] 3',5'-bispyrophosphate: a model for programmed bacterial cell death. Proc. Natl. Acad. Sci. USA 1996, 93, 6059-6063.
79. Lee, S., Kim, M. H., Kang, B. S., Kim, J.-S. et al., Crystal Structure of Escherichia coli MazG, the regulator of nutritional stress response. J. Biol. Chem. 2008, 283, 15232-15240.
80. Kvint, K., Nachin, L., Diez, A., Nyström, T., The bacterial universal stress protein: function and regulation. Curr. Opin. Microbiol. 2003, 6, 140-145.
81. Kashiwagi, K., Yamaguchi, Y., Sakai, Y., Kobayashi, H., Igarashi, K., Identification of the polyamine-induced protein as a periplasmic oligopeptide binding protein. J. Biol. Chem. 1990, 265, 8387-8391.
82. Van Hove, B., Staudenmaier, H., Braun, V., Novel two-component transmembrane transcription control: regulation of iron dicitrate transport in Escherichia coli K-12. J. Bacteriol. 1990, 172, 6749-6758.
83. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., Kuster, B., Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 2007, 389, 1017-1031.
84. Hall, D. A., Zhu, H., Zhu, X., Royce, T. et al., Regulation of gene expression by a metabolic enzyme. Science 2004, 306, 482-484.
85. Jeffery, C. J., Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins. Curr. Opin. Struct. Biol. 2004, 14, 663-668.
86. Shi, Y., Shi, Y., Metabolic enzymes and coenzymes in transcription-a direct link between metabolism and transcription? Trends Genet. 2004, 20, 445-452.
87. Cunningham, L., Gruer, M. J., Guest, J. R., Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli. Microbiology 1997, 143, 3795-3805.
88. Stancik, L. M., Stancik, D. M., Schmidt, B., Barnhart, D. M. et al., pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli. J. Bacteriol. 2002, 184, 4246-4258.
89. Song, J. A., Han, K. Y., Park, J. S., Seo, H. S. et al., Human G-CSF synthesis using stress-responsive bacterial proteins. FEMS Microbiol. Lett. 2009, 296, 60-66.
90. Zhou, Y., Zhu, W., Bellur, P. S., Rewinkel, D., Becker, D. F., Direct linking of metabolism and gene expression in the proline utilization A protein from Escherichia coli. Amino Acids 2008, 35, 711-718.
91. Storz, G., Imlay, J. A., Oxidative stress. Curr. Opin. Microbiol. 1999, 2, 188-194.
92. Carpousis, A. J., The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu. Rev. Microbiol. 2007, 61, 71-87.
93. Bubunenko, M., Baker, T., Court, D. L., Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J. Bacteriol. 2007, 189, 2844-2853.
94. Harinarayanan, R., Gowrishankar, J., Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli. J. Mol. Biol. 2003, 332, 31-46.
95. Kirsebom, L. A., Amons, R., Isaksson, L. A., Primary structures of mutationally altered ribosomal protein L7/L12 and their effects on cellular growth and translational accuracy. Eur. J. Biochem. 1986, 156, 669-675.
96. Ellis, R. J., Revisiting the Anfinsen cage. Fold. Des. 1996, 1, R9-R15.