Differential transcriptional response to antibiotics by Pseudomonas putidaDOT-T1E

Environmental Microbiology

Volumn 17, Issue 9, 2015, Pages 3251-3262

  Molina Santiago, Carlos ^a   Daddaoua, Abdelali ^a   Gómez Lozano, María ^b   Udaondo, Zulema ^a,c   Molin, Søren ^b   Ramos, Juan Luis ^a,c  

^a CSIC   (Spain)

^b Chalmers University of Technology   (Denmark)

^c ABENGOA RESEARCH   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT; MESSENGER RNA; SMALL UNTRANSLATED RNA; SOLVENT;

DRUG EFFECTS; GENETIC TRANSCRIPTION; GENETICS; MULTIDRUG RESISTANCE; PSEUDOMONAS PUTIDA;

ANTI-BACTERIAL AGENTS; DRUG RESISTANCE, MULTIPLE, BACTERIAL; PSEUDOMONAS PUTIDA; RNA, MESSENGER; RNA, SMALL UNTRANSLATED; SOLVENTS; TRANSCRIPTION, GENETIC;

EID: 84941022256     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12775     Document Type: Article

References (52)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Arias, C.A., and Murray, B.E. (2009) Antibiotic-resistant bugs in the 21st century - a clinical super-challenge. N Engl J Med 360: 439-443.
3. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., etal. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
4. Benjamini, Y., Drai, D., Elmer, G., Kafkafi, N., and Golani, I. (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125: 279-284.
5. Cameron, J.C., and Pakrasi, H.B. (2011) Glutathione facilitates antibiotic resistance and photosystem I stability during exposure to gentamicin in cyanobacteria. Appl Environ Microbiol 77: 3547-3550.
6. Connell, S.R., Tracz, D.M., Nierhaus, K.H., and Taylor, D.E. (2003) Ribosomal protection proteins and their mechanism of tetracycline resistance. Antimicrob Agents Chemother 47: 3675-3681.
7. Daddaoua, A., Krell, T., and Ramos, J.L. (2013) Transcriptional control by two interacting regulatory proteins: identification of the PtxS binding site at PtxR. Nucleic Acids Res 41: 10150-10156.
8. D'Costa, V.M., McGrann, K.M., Hughes, D.W., and Wright, G.D. (2006) Sampling the antibiotic resistome. Science 311: 374-377.
9. Dos Santos, V.A., Heim, S., Moore, E.R., Stratz, M., and Timmis, K.N. (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6: 1264-1286.
10. Drlica, K., and Zhao, X. (1997) DNA gyrase, topoisomerase IV, and the 4-quinolones. Microbiol Mol Biol Rev 61: 377-392.
11. Duque, E., Rodriguez-Herva, J.J., de la Torre, J., Dominguez-Cuevas, P., Munoz-Rojas, J., and Ramos, J.L. (2007) The RpoT regulon of Pseudomonas putida DOT-T1E and its role in stress endurance against solvents. J Bacteriol 189: 207-219.
12. Eudes, A., Erkens, G.B., Slotboom, D.J., Rodionov, D.A., Naponelli, V., and Hanson, A.D. (2008) Identification of genes encoding the folate- and thiamine-binding membrane proteins in Firmicutes. J Bacteriol 190: 7591-7594.
13. Fernández, M., Conde, S., de la Torre, J., Molina-Santiago, C., Ramos, J.L., and Duque, E. (2012a) Mechanisms of resistance to chloramphenicol in Pseudomonas putida KT2440. Antimicrob Agents Chemother 56: 1001-1009.
14. Fernández, M., Niqui-Arroyo, J.L., Conde, S., Ramos, J.L., and Duque, E. (2012b) Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid. Appl Environ Microbiol 78: 5104-5110.
15. Fernandes, P. (2006) Antibacterial discovery and development - the failure of success? Nat Biotechnol 24: 1497-1503.
16. Fillet, S., Daniels, C., Pini, C., Krell, T., Duque, E., Bernal, P., etal. (2012) Transcriptional control of the main aromatic hydrocarbon efflux pump in Pseudomonas. Environ Microbiol Rep 4: 158-167.
17. Gomez-Lozano, M., Marvig, R.L., Molin, S., and Long, K.S. (2012) Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa. Environ Microbiol 14: 2006-2016.
18. Gomez-Lozano, M., Marvig, R.L., Molin, S., and Long, K.S. (2014) Identification of bacterial small RNAs by RNA sequencing. Methods Mol Biol 1149: 433-456.
19. Hahn, F.E., Wisseman, C.L., Jr, and Hopps, H.E. (1955) Mode of action of chloramphenicol. III. Action of chloramphenicol on bacterial energy metabolism. J Bacteriol 69: 215-223.
20. Heo, A., Jang, H.J., Sung, J.S., and Park, W. (2014) Global transcriptome and physiological responses of Acinetobacter oleivorans DR1 exposed to distinct classes of antibiotics. PLoS ONE 9: e110215.
21. Herrera, M.C., Daddaoua, A., Fernández-Escamilla, A., and Ramos, J.L. (2012) Involvement of the global Crp regulator in cyclic AMP-dependent utilization of aromatic amino acids by Pseudomonas putida. J Bacteriol 194: 406-412.
22. Howden, B.P., Beaume, M., Harrison, P.F., Hernandez, D., Schrenzel, J., Seemann, T., etal. (2013) Analysis of the small RNA transcriptional response in multidrug-resistant Staphylococcus aureus after antimicrobial exposure. Antimicrob Agents Chemother 57: 3864-3874.
23. Kang, T.M., Yuan, J., Nguyen, A., Becket, E., Yang, H., and Miller, J.H. (2012) The aminoglycoside antibiotic kanamycin damages DNA bases in Escherichia coli: caffeine potentiates the DNA-damaging effects of kanamycin while suppressing cell killing by ciprofloxacin in Escherichia coli and Bacillus anthracis. Antimicrob Agents Chemother 56: 3216-3223.
24. Kehrenberg, C., and Schwarz, S. (2007) Mutations in 16S rRNA and ribosomal protein S5 associated with high-level spectinomycin resistance in Pasteurella multocida. Antimicrob Agents Chemother 51: 2244-2246.
25. de Knegt, G.J., Bruning, O., ten Kate, M.T., de Jong, M., van Belkum, A., Endtz, H.P., etal. (2013) Rifampicin-induced transcriptome response in rifampicin-resistant Mycobacterium tuberculosis. Tuberculosis (Edinb) 93: 96-101.
26. Kohanski, M.A., Dwyer, D.J., and Collins, J.J. (2010) How antibiotics kill bacteria: from targets to networks. Nat Rev Microbiol 8: 423-435.
27. Lange, R.P., Locher, H.H., Wyss, P.C., and Then, R.L. (2007) The targets of currently used antibacterial agents: lessons for drug discovery. Curr Pharm Des 13: 3140-3154.
28. Levine, E., Zhang, Z., Kuhlman, T., and Hwa, T. (2007) Quantitative characteristics of gene regulation by small RNA. PLoS Biol 5: e229.
29. McClure, R., Balasubramanian, D., Sun, Y., Bobrovskyy, M., Sumby, P., Genco, C.A., etal. (2013) Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res 41: e140.
30. Maddocks, S.E., and Oyston, P.C. (2008) Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154: 3609-3623.
31. Misumi, M., and Tanaka, N. (1980) Mechanism of inhibition of translocation by kanamycin and viomycin: a comparative study with fusidic acid. Biochem Biophys Res Commun 92: 647-654.
32. Molina, L., Udaondo, Z., Duque, E., Fernández, M., Molina-Santiago, C., Roca, A., etal. (2014) Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital. PLoS ONE 9: e81604.
33. Molina-Santiago, C., Daddaoua, A., Fillet, S., Duque, E., and Ramos, J.L. (2014a) Interspecies signalling: Pseudomonas putida efflux pump TtgGHI is activated by indole to increase antibiotic resistance. Environ Microbiol 16: 1267-1281.
34. Molina-Santiago, C., Daddaoua, A., Fillet, S., Krell, T., Morel, B., Duque, E., and Ramos, J.L. (2014b) Identification of new residues involved in intramolecular signal transmission in a prokaryotic transcriptional repressor. J Bacteriol 196: 588-594.
35. Moore, E.B., Tindall, B., Martins Dos Santos, V.P., Pieper, D., Ramos, J.-L., and Palleroni, N. (2006) Nonmedical: Pseudomonas. In The Prokaryotes. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds). New York, USA: Springer, pp. 646-703.
36. Patkari, M., and Mehra, S. (2013) Transcriptomic study of ciprofloxacin resistance in Streptomyces coelicolor A3(2). Mol Biosyst 9: 3101-3116.
37. Pestka, S. (1975) The use of inhibitors in studies on protein synthesis. In Methods in Enzymology. Moldave, K., Grossman, L., and Academic Press (eds). New York, USA: Springer, pp. 261-282.
38. Pommier, Y., Leo, E., Zhang, H., and Marchand, C. (2010) DNA topoisomerases and their poisoning by anticancer and antibacterial drugs. Chem Biol 17: 421-433.
39. Ramos, J.L., Duque, E., Huertas, M.J., and Haidour, A. (1995) Isolation and expansion of the catabolic potential of a Pseudomonas putida strain able to grow in the presence of high concentrations of aromatic hydrocarbons. J Bacteriol 177: 3911-3916.
40. Ramos, J.L., Duque, E., Godoy, P., and Segura, A. (1998) Efflux pumps involved in toluene tolerance in Pseudomonas putida DOT-T1E. J Bacteriol 180: 3323-3329.
41. Rojas, A., Duque, E., Mosqueda, G., Golden, G., Hurtado, A., Ramos, J.L., and Segura, A. (2001) Three efflux pumps are required to provide efficient tolerance to toluene in Pseudomonas putida DOT-T1E. J Bacteriol 183: 3967-3973.
42. Stjepandic, D., Weinel, C., Hilbert, H., Koo, H.L., Diehl, F., Nelson, K.E., etal. (2002) The genome structure of Pseudomonas putida: high-resolution mapping and microarray analysis. Environ Microbiol 4: 819-823.
43. Storz, G., Vogel, J., and Wassarman, K.M. (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43: 880-891.
44. Suzek, B.E., Huang, H., McGarvey, P., Mazumder, R., and Wu, C.H. (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23: 1282-1288.
45. Terán, W., Felipe, A., Segura, A., Rojas, A., Ramos, J.L., and Gallegos, M.T. (2003) Antibiotic-dependent induction of Pseudomonas putida DOT-T1E TtgABC efflux pump is mediated by the drug binding repressor TtgR. Antimicrob Agents Chemother 47: 3067-3072.
46. Tropel, D., and van der Meer, J.R. (2004) Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev 68: 474-500.
47. Waters, L.S., and Storz, G. (2009) Regulatory RNAs in bacteria. Cell 136: 615-628.
48. Weinstein, M.J., Wagman, G.H., Oden, E.M., and Marquez, J.A. (1967) Biological activity of the antibiotic components of the gentamicin complex. J Bacteriol 94: 789-790.
49. Wolfe, A.D., and Hahn, F.E. (1965) Mode of action of chloramphenicol. Ix. Effects of chloramphenicol upon a ribosomal amino acid polymerization system and its binding to bacterial ribosome. Biochim Biophys Acta 95: 146-155.
50. Ye, J., Fang, L., Zheng, H., Zhang, Y., Chen, J., Zhang, Z., etal. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34: W293-W297.
51. Yu, J., and Schneiders, T. (2012) Tigecycline challenge triggers sRNA production in Salmonella enterica serovar Typhimurium. BMC Microbiol 12: 195.
52. Zakeri, B., and Wright, G.D. (2008) Chemical biology of tetracycline antibiotics. Biochem Cell Biol 86: 124-136.