Understanding butanol tolerance and assimilation in Pseudomonas putidaBIRD-1: An integrated omics approach

Microbial Biotechnology

Volumn 9, Issue 1, 2016, Pages 100-115

  Cuenca, María del Sol ^a   Roca, Amalia ^b   Molina Santiago, Carlos ^a   Duque, Estrella ^a   Armengaud, Jean ^c   Gómez Garcia, María R ^a   Ramos, Juan L ^a  

^a ABENGOA RESEARCH   (Spain)

^b Bio Iliberis R and D Polígono Juncaril ^*  (Spain)

^c DIF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACYL COENZYME A DEHYDROGENASE; ALDEHYDE DEHYDROGENASE; BUTANOL; GLYOXYLIC ACID; ISOCITRATE LYASE; LONG CHAIN FATTY ACID COENZYME A LIGASE; ACETATE COENZYME A LIGASE; BACTERIAL PROTEIN;

ALCOHOL TOLERANCE; ARTICLE; CARBON SOURCE; CITRIC ACID CYCLE; CONTROLLED STUDY; DEFENSE MECHANISM; ENZYME METABOLISM; FATTY ACID METABOLISM; FUNGAL GENE; FUNGAL GENOME; FUNGAL STRAIN; MOLECULAR CLONING; NONHUMAN; OXIDATION REDUCTION STATE; PROTEIN LOCALIZATION; PROTEOMICS; PSEUDOMONAS PUTIDA; SIGNAL TRANSDUCTION; TRANSCRIPTOMICS; TRANSPOSON; UPREGULATION; ENZYMOLOGY; GENETICS; METABOLISM;

ACETATE-COA LIGASE; ACYL-COA DEHYDROGENASES; BACTERIAL PROTEINS; BUTANOLS; PROTEOMICS; PSEUDOMONAS PUTIDA;

EID: 84953266666     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/1751-7915.12328     Document Type: Article

References (53)

1. Abril, M.A., Michan, C., Timmis, K.N., and Ramos, J.L. (1989) Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway. J Bacteriol 171: 6782-6790.
2. Arp, D.J. (1999) Butane metabolism by butane-grown Pseudomonas butanovora. Microbiology 145: 1173-1180.
3. Atsumi, S., Cann, A.F., Connor, M.R., Shen, C.R., Smith, K.M., Brynildsen, M.P., etal. (2008) Metabolic engineering of Escherichia coli for 1-butanol production. Metab Eng 10: 305-311.
4. Benjamini, Y., and Yekutieli, D. (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29: 1165-1188.
5. Berezina, O.V., Zakharova, N.V., Brandt, A., Yarotsky, S.V., Schwarz, W.H., and Zverlov, V.V. (2010) Reconstructing the clostridial n-butanol metabolic pathway in Lactobacillus brevis. Appl Microbiol Biotechnol 87: 635-646.
6. Brynildsen, M.P., and Liao, J.C. (2009) An integrated network approach identifies the isobutanol response network of Escherichia coli. Molecular System Biology 277: 1-13.
7. Caballero, V.C., Toledo, V.P., Maturana, C., Fisher, C.R., Payne, S.M., and Salazar, J.C. (2012) Expression of Shigella flexneri gluQ-rs gene is linked to dksA and controlled by a transcriptional terminator. BMC Microbiol 12: 226.
8. Caetano-Anolles, G. (1993) Amplifying DNA with arbitrary oligonucleotide primers. PCR Methods Appl 3: 85-94.
9. Carvalho, P., Fischer, J., Chen, E., Yates, J., and Barbosa, V. (2008) PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics 9: 316.
10. Carvalho, P.C., Yates, J.R., and Barbosa, V.C. (2012) Improving the TFold test for differential shotgun proteomics. Bioinformatics 28: 1652-1654.
11. Cascone, R. (2008) Biobutanol: A Replacement for Bioethanol? New York, NY, USA: American Institute of Chemical Engineers.
12. Christie-Oleza, J.A., Fernandez, B., Nogales, B., Bosch, R., and Armengaud, J. (2012a) Proteomic insights into the lifestyle of an environmentally relevant marine bacterium. ISME J 6: 124-135.
13. Christie-Oleza, J.A., Pina-Villalonga, J.M., Bosch, R., Nogales, B., and Armengaud, J. (2012b) Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria. Mol Cell Proteomics 11: 12-23.
14. Clair, G., Armengaud, J., and Duport, C. (2012) Restricting fermentative potential by proteome remodeling: an adaptive strategy evidenced in Bacillus cereus. Mol Cell Proteomics 11. doi: 10.1074/mcp.M111.013102.
15. Dominguez-Cuevas, P., Gonzalez-Pastor, J.E., Marques, S., Ramos, J.L., and de Lorenzo, V. (2006) Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J Biol Chem 281: 11981-11991.
16. Dupierris, V., Masselon, C., Court, M., Kieffer-Jaquinod, S., and Bruley, C. (2009) A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa. Bioinformatics 25: 1980-1981.
17. Dürre, P. (2011) Fermentative production of butanol: the academic perspective. Curr Opin Biotechnol 22: 331-336.
18. Ezeji, T.C., Qureshi, N., and Blaschek, H.P. (2007) Bioproduction of butanol from biomass: from genes to bioreactors. Curr Opin Biotechnol 18: 220-227.
19. Filloux, A.R.J.L. (2014) Pseudomonas: Methods and Protocols. New York, USA; Springer.
20. Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., etal. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41: D808-D815.
21. Gentry, D.R., and Cashel, M. (1996) Mutational analysis of the Escherichia coli spoT gene identifies distinct but overlapping regions involved in ppGpp synthesis and degradation. Mol Microbiol 19: 1373-1384.
22. Gomez-Lozano, M., Marvig, R., Tulstrup, M., and Molin, S. (2014) Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa. BMC Genomics 15: 783.
23. Green, E.M. (2011) Fermentative production of butanol - the industrial perspective. Curr Opin Biotechnol 22: 337-343.
24. Guazzaroni, M.E., Krell, T., Felipe, A., Ruiz, R., Meng, C., Zhang, X., etal. (2005) The multidrug efflux regulator TtgV recognizes a wide range of structurally different effectors in solution and complexed with target DNA: evidence from isothermal titration calorimetry. J Biol Chem 280: 20887-20893.
25. Gulevich, A., Skorokhodova, A., Sukhozhenko, A., Shakulov, R., and Debabov, V. (2012) Metabolic engineering of Escherichia coli for 1-butanol biosynthesis through the inverted aerobic fatty acid β-oxidation pathway. Biotechnol Lett 34: 463-469.
26. Hartmann, E.M., and Armengaud, J. (2014) Shotgun proteomics suggests involvement of additional enzymes in dioxin degradation by Sphingomonas wittichii RW1. Environ Microbiol 16: 162-176.
27. Lin, P.P., Rabe, K.S., Takasumi, J.L., Kadisch, M., Arnold, F.H., and Liao, J.C. (2014) Isobutanol production at elevated temperatures in thermophilic Geobacillus thermoglucosidasius. Metab Eng 24: 1-8.
28. Llamas, M.A., Rodriguez-Herva, J.J., Hancock, R.E., Bitter, W., Tommassen, J., and Ramos, J.L. (2003) Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane. J Bacteriol 185: 4707-4716.
29. de Lorenzo, V., and Timmis, K.N. (1994) Analysis and construction of stable phenotypes in gram-negative bacteria with Tn5- and Tn10-derived minitransposons. Methods Enzymol 235: 386-405.
30. 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.
31. Madhusudhan, K.T., Lorenz, D., and Sokatch, J.R. (1993) The bkdR gene of Pseudomonas putida is required for expression of the bkd operon and encodes a protein related to Lrp of Escherichia coli. J Bacteriol 175: 3934-3940.
32. Martinez-Granero, F., Redondo-Nieto, M., Vesga, P., Martin, M., and Rivilla, R. (2014) AmrZ is a global transcriptional regulator implicated in iron uptake and environmental adaption in P. fluorescens F113. BMC Genomics 15: 237.
33. Mathew, R., Ramakanth, M., and Chatterji, D. (2005) Deletion of the gene rpoZ, encoding the α subunit of RNA polymerase, in Mycobacterium smegmatis results in fragmentation of the ß' subunit in the enzyme assembly. J Bacteriol 187: 6565-6570.
34. Matilla, M.A., Pizarro-Tobias, P., Roca, A., Fernandez, M., Duque, E., Molina, L.Z., etal. (2011) Complete genome of the plant growth-promoting rhizobacterium Pseudomonas putida BIRD-1. J Bacteriol 193: 1290.
35. Molina-Santiago, C., Daddaoua, A., Fillet, S., Duque, E., and Ramos, J.-L. (2014) Interspecies signalling: pseudomonas putida efflux pump TtgGHI is activated by indole to increase antibiotic resistance. Environ Microbiol 16: 1267-1281.
36. Mukherjee, K., Nagai, H., Shimamoto, N., and Chatterji, D. (1999) GroEL is involved in activation of Escherichia coli RNA polymerase devoid of the ω subunit in vivo. Eur J Biochem 266: 228-235.
37. Nakazawa, T. (2002) Travels of a Pseudomonas, from Japan around the world. Environ Microbiol 4: 782-786.
38. Nielsen, D.R., Leonard, E., Yoon, S.-H., Tseng, H.-C., Yuan, C., and Prather, K.L.J. (2009) Engineering alternative butanol production platforms in heterologous bacteria. Metab Eng 11: 262-273.
39. O'Toole, G.A., and Kolter, R. (1998) Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis. Mol Microbiol 28: 449-461.
40. Papoutsakis, E.T., and Alsaker, K.V. (2012) Towards a synthetic biology of the stress-response and the tolerance phenotype: systems understanding and engineering of the Clostridium acetobutylicum stress-response and tolerance to toxic metabolites. In Systems Metabolic Engineering. Netherlands: Springer, pp. 193-219.
41. Ramos, J.-L., Filloux, A., Duque, E., Molina-Henares, A., Torre, J.S., Molina-Henares, M.A., etal. (2007) Towards a genome-wide mutant library of Pseudomonas putida strain KT2440. In Pseudomonas. Netherlands: Springer, 227-251.
42. 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.
43. Ramos, J.L., Duque, E., Rodriguez-Herva, J.J., Godoy, P., Haidour, A., Reyes, F., and Fernandez-Barrero, A. (1997) Mechanisms for solvent tolerance in bacteria. J Biol Chem 272: 3887-3890.
44. 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.
45. Ramos, J.L., Duque, E., Gallegos, M.T., Godoy, P., Ramos-Gonzalez, M.I., Rojas, A., etal. (2002) Mechanisms of solvent tolerance in gram-negative bacteria. Annu Rev Microbiol 56: 743-768.
46. Ramos, J.L., Martinez-Bueno, M., Molina-Henares, A.J., Teran, W., Watanabe, K., Zhang, X., etal. (2005) The TetR family of transcriptional repressors. Microbiol Mol Biol Rev 69: 326-356.
47. Ramos, J.L., Sol Cuenca, M., Molina-Santiago, C., Segura, A., Duque, E., Gomez-Garcia, M.R., etal. (2015) Mechanisms of solvent resistance mediated by interplay of cellular factors in Pseudomonas putida. FEMS Microbiol Rev. doi: 10.1007/s00253-015-6963-9.
48. Reyes, L.H., Almario, M.P., and Kao, K.C. (2011) Genomic library screens for genes involved in n-butanol tolerance in Escherichia coli. PLoS ONE 6: e17678.
49. Robinson, J.T., Thorvaldsdottir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G., and Mesirov, J.P. (2011) Integrative genomics viewer. Nat Biotechnol 29: 24-26.
50. Rutherford, B.J., Dahl, R.H., Price, R.E., Szmidt, H.L., Benke, P.I., Mukhopadhyay, A., and Keasling, J.D. (2010) Functional genomic study of exogenous n-butanol stress in Escherichia coli. Appl Environ Microbiol 76: 1935-1945.
51. Schiel-Bengelsdorf, B., Montoya, J., Linder, S., and Dürre, P. (2013) Butanol fermentation. Environ Technol 34: 1691-1710.
52. Steen, E., Chan, R., Prasad, N., Myers, S., Petzold, C., Redding, A., etal. (2008) Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb Cell Fact 7: 1-8.
53. Udaondo, Z., Duque, E., Fernández, M., Molina, L., Torre, J.D.L., Bernal, P., etal. (2012) Analysis of solvent tolerance in Pseudomonas putida DOT-T1E based on its genome sequence and a collection of mutants. FEBS Lett 586: 2932-2938.