The interplay of the EIIANtr component of the nitrogen-related phosphotransferase system (PTSNtr) of Pseudomonas putida with pyruvate dehydrogenase

Biochimica et Biophysica Acta - General Subjects

Volumn 1810, Issue 10, 2011, Pages 995-1005

  Pflüger Grau, Katharina ^a,b   Chavarría, Max ^a   De Lorenzo, Víctor ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Biodegradation; Catabolic repression; Metabolic control; Pseudomonas putida; PTS; Pyruvate dehydrogenase

Indexed keywords

BACTERIAL PROTEIN; CARBOHYDRATE; CARBON; CYTOPLASM PROTEIN; EPITOPE; MONOCLONAL ANTIBODY; MONOCLONAL ANTIBODY E; NITROGEN; NITROGEN RELATED PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE; PROTEIN EIIA; PYRUVATE DEHYDROGENASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL CELL; CITRIC ACID CYCLE; CONTROLLED STUDY; CYTOPLASM; ENZYME ACTIVITY; ENZYME INHIBITION; ENZYME REGULATION; GENE SEQUENCE; IMMUNOPRECIPITATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PSEUDOMONAS PUTIDA;

BACTERIAL PROTEINS; BLOTTING, WESTERN; IMMUNOPRECIPITATION; KETONE OXIDOREDUCTASES; MICROSCOPY, CONFOCAL; PHOSPHOENOLPYRUVATE SUGAR PHOSPHOTRANSFERASE SYSTEM; PROTEIN BINDING; PSEUDOMONAS PUTIDA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

BACTERIA (MICROORGANISMS); PSEUDOMONAS PUTIDA;

EID: 80052067349     PISSN: 03044165     EISSN: 18728006     Source Type: Journal    
DOI: 10.1016/j.bbagen.2011.01.002     Document Type: Article

References (72)

1. D.H. Pieper, V.A. Martins dos Santos, and P.N. Golyshin Genomic and mechanistic insights into the biodegradation of organic pollutants Curr. Opin. Biotechnol. 15 2004 215 224 (Pubitemid 38750253)
2. D.H. Pieper, and W. Reineke Engineering bacteria for bioremediation Curr. Opin. Biotechnol. 11 2000 262 270 (Pubitemid 30326473)
3. I. Cases, and V. de Lorenzo Genetically modified organisms for the environment: stories of success and failure and what we have learned from them Int. Microbiol. 8 2005 213 222 (Pubitemid 41322272)
4. V. de Lorenzo Systems biology approaches to bioremediation Curr. Opin. Biotechnol. 19 2008 579 589
5. R. Vilchez-Vargas, H. Junca, and D.H. Pieper Metabolic networks, microbial ecology and 'omics' technologies: towards understanding in situ biodegradation processes Environ. Microbiol. 12 2010 3089 3104
6. P.W. Postma, J.W. Lengeler, and G.R. Jacobson Phosphoenolpyruvate: carbohydrate phosphotransferase systems of bacteria Microbiol. Rev. 57 1993 543 594
7. M.H. Saier Jr., and J. Reizer The bacterial phosphotransferase system: new frontiers 30 years later Mol. Microbiol. 13 1994 755 764 (Pubitemid 24272196)
8. J.H. Tchieu, V. Norris, J.S. Edwards, and M.H. Saier Jr. The complete phosphotranferase system in Escherichia coli J. Mol. Microbiol. Biotechnol. 3 2001 329 346 (Pubitemid 32421653)
9. I. Cases, F. Velázquez, and V. de Lorenzo The ancestral role of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) as exposed by comparative genomics Res. Microbiol. 158 2007 666 670 (Pubitemid 350213375)
10. R.D. Barabote, and M.H. Saier Jr. Comparative genomic analyses of the bacterial phosphotransferase system Microbiol. Mol. Biol. Rev. 69 2005 608 634 (Pubitemid 41798465)
11. K. Pflüger, and V. de Lorenzo Growth-dependent phosphorylation of the PtsN (EIINtr) protein of Pseudomonas putida J. Biol. Chem. 282 2007 18206 18211 (Pubitemid 47100224)
12. J. Reizer, A. Reizer, M.H. Saier Jr., and G.R. Jacobson A proposed link between nitrogen and carbon metabolism involving protein phosphorylation in bacteria Protein Sci. 1 1992 722 726 (Pubitemid 23007311)
13. I. Cases, and V. de Lorenzo Genetic evidence of distinct physiological regulation mechanisms in the sigma(54) Pu promoter of Pseudomonas putida J. Bacteriol. 182 2000 956 960 (Pubitemid 30075017)
14. I. Cases, J. Pérez-Martín, and V. de Lorenzo The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source inhibition of the sigma54-dependent Pu promoter of the TOL plasmid J. Biol. Chem. 274 1999 15562 15568
15. I. Cases, F. Velázquez, and V. de Lorenzo Role of ptsO in carbon-mediated inhibition of the Pu promoter belonging to the pWW0 Pseudomonas putida plasmid J. Bacteriol. 183 2001 5128 5133 (Pubitemid 32750941)
16. T. del Castillo, J.L. Ramos, J.J. Rodriguez-Herva, T. Fuhrer, U. Sauer, and E. Duque Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis J. Bacteriol. 189 2007 5142 5152 (Pubitemid 47076060)
17. T. del Castillo, and J.L. Ramos Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways J. Bacteriol. 189 2007 6602 6610 (Pubitemid 47397366)
18. K. Pflüger, and V. de Lorenzo Evidence of in vivo cross talk between the nitrogen-related and fructose-related branches of the carbohydrate phosphotransferase system of Pseudomonas putida J. Bacteriol. 190 2008 3374 3380 (Pubitemid 351581433)
19. C.R. Lee, S.H. Cho, M.J. Yoon, A. Peterkofsky, and Y.J. Seok Escherichia coli enzyme IIANtr regulates the K+ transporter TrkA Proc. Natl Acad. Sci. USA 104 2007 4124 4129 (Pubitemid 47181589)
20. D. Lüttmann, R. Heermann, B. Zimmer, A. Hillmann, I.S. Rampp, K. Jung, and B. Görke Stimulation of the potassium sensor KdpD kinase activity by interaction with the phosphotransferase protein IIA(Ntr) in Escherichia coli Mol. Microbiol. 72 2009 978 994
21. N.D. King, and M.R. O'Brian Evidence for direct interaction between enzyme I(Ntr) and aspartokinase to regulate bacterial oligopeptide transport J. Biol. Chem. 276 2001 21311 21316
22. F. Pompeo, J. Luciano, and A. Galinier Interaction of GapA with HPr and its homologue, Crh: novel levels of regulation of a key step of glycolysis in Bacillus subtilis? J. Bacteriol. 189 2007 1154 1157 (Pubitemid 46183892)
23. S. Fernandez, V. de Lorenzo, and J. Peréz-Martin Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains Mol. Microbiol. 16 1995 205 213
24. V. de Lorenzo, L. Eltis, B. Kessler, and K.N. Timmis Analysis of Pseudomonas gene products using lacIq/Ptrp-lac plasmids and transposons that confer conditional phenotypes Gene 123 1993 17 24 (Pubitemid 23035786)
25. K. Pflüger, I. di Bartolo, F. Velázquez, and V. de Lorenzo Non-disruptive release of Pseudomonas putida proteins by in situ electric breakdown of intact cells J. Microbiol. Methods 71 2007 179 185 (Pubitemid 350153649)
26. E. Moreno-Ruiz, M.J. Hernáez, O. Martínez-Pérez, and E. Santero Identification and functional characterization of Sphingomonas macrogolitabida strain TFA genes involved in the first two steps of the tetralin catabolic pathway J. Bacteriol. 185 2003 2026 2030 (Pubitemid 36297905)
27. M.E. Kovach, P.H. Elzer, D.S. Hill, G.T. Robertson, M.A. Farris, R.M. Roop 2nd, and K.M. Peterson Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes Gene 166 1995 175 176
28. D. Kleiner, W. Paul, and M.J. Merrick Construction of multicopy expression vectors for regulated over-production of proteins in Klebsiella pneumoniae and other enteric bacteria J. Gen. Microbiol. 134 1988 1779 1784
29. V. de Lorenzo, and K.N. Timmis Analysis and construction of stable phenotypes in Gram-negative bacteria with Tn5- and Tn10-derived minitransposons Meth. Enzymol. 235 1994 386 405
30. J. Sambrook, E.F. Fritsch, and T. Maniatis Molecular cloning: a laboratory manual 1989 Cold Spring Harbor
31. G. Posfai, V. Kolisnychenko, Z. Bereczki, and F.R. Blattner Markerless gene replacement in Escherichia coli stimulated by a double-strand break in the chromosome Nucleic Acids Res. 27 1999 4409 4415 (Pubitemid 29533182)
32. R.J. Penfold, and J.M. Pemberton An improved suicide vector for construction of chromosomal insertion mutations in bacteria Gene 118 1992 145 146
33. G. Demarre, A.M. Guerout, C. Matsumoto-Mashimo, D.A. Rowe-Magnus, P. Marliere, and D. Mazel A new family of mobilizable suicide plasmids based on broad host range R388 plasmid (IncW) and RP4 plasmid (IncPalpha) conjugative machineries and their cognate Escherichia coli host strains Res. Microbiol. 156 2005 245 255 (Pubitemid 40320963)
34. P. Jurado, D. Ritz, J. Beckwith, V. de Lorenzo, and L.A. Fernandez Production of functional single-chain Fv antibodies in the cytoplasm of Escherichia coli J. Mol. Biol. 320 2002 1 10 (Pubitemid 34722230)
35. F. Ausubel, R. Brent, R. Kingston, D. Moore, J. Seidman, J. Smith, and K. Struhl Current protocols in molecular biology 1993
36. A. Shevchenko, M. Wilm, O. Vorm, and M. Mann Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels Anal. Chem. 68 1996 850 858
37. M.S. Sosa, M.R. Girotti, E. Salvatierra, F. Prada, J.A. de Olmo, S.J. Gallango, J.P. Albar, O.L. Podhajcer, and A.S. Llera Proteomic analysis identified N-cadherin, clusterin, and HSP27 as mediators of SPARC (secreted protein, acidic and rich in cysteines) activity in melanoma cells Proteomics 7 2007 4123 4134 (Pubitemid 350190284)
38. D.C. Pauling, J.P. Lapointe, C.M. Paris, and R.A. Ludwig Azorhizobium caulinodans pyruvate dehydrogenase activity is dispensable for aerobic but required for microaerobic growth Microbiology 147 2001 2233 2245 (Pubitemid 32785503)
39. M.M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 72 1976 248 254
40. H. Hajjaj, P. Blanc, G. Goma, and J. François Sampling techniques and comparative extraction procedures for quantitative determination of intra- and extracellular metabolites in filamentous fungi FEMS Microbiol. Lett. 164 1998 195 200 (Pubitemid 28308315)
41. T. Fuhrer, and U. Sauer Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism J. Bacteriol. 191 2009 2112 2121
42. L. Gao, W. Chiou, H. Tang, X. Cheng, H.S. Camp, and D.J. Burns Simultaneous quantification of malonyl-CoA and several other short-chain acyl-CoAs in animal tissues by ion-pairing reversed-phase HPLC/MS J. Chromatogr. B Analy. Technol. Biomed. Life Sci. 853 2007 303 313 (Pubitemid 46891368)
43. M.V. Baev, D. Baev, A.J. Radek, and J.W. Campbell Growth of Escherichia coli MG1655 on LB medium: monitoring utilization of sugars, alcohols, and organic acids with transcriptional microarrays Appl. Microbiol. Biotechnol. 71 2006 310 316 (Pubitemid 43962135)
44. B. Powell, D. Court, T. Inada, Y. Nakamura, V. Michotey, X. Cui, A. Reizer, M. Saier, and J. Reizer Novel proteins of the phosphotransferase system encoded within the rpoN operon of Escherichia coli. Enzyme IIANtr affects growth on organic nitrogen and the conditional lethality of an erats mutant J. Biol. Chem. 270 1995 4822 4839
45. J. Deutscher, C. Francke, and P.W. Postma How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria Microbiol. Mol. Biol. Rev. 70 2006 939 1031 (Pubitemid 44958262)
46. G. Butland, J.M. Peregrin-Alvarez, J. Li, W. Yang, X. Yang, V. Canadien, A. Starostine, D. Richards, B. Beattie, N. Krogan, M. Davey, J. Parkinson, J. Greenblatt, and A. Emili Interaction network containing conserved and essential protein complexes in Escherichia coli Nature 433 2005 531 537 (Pubitemid 40204311)
47. A. de Kok, A.F. Hengeveld, A. Martin, and A.H. Westphal The pyruvate dehydrogenase multi-enzyme complex from Gram-negative bacteria Biochim. Biophys. Acta 1385 1998 353 366 (Pubitemid 28310799)
48. H. Biswanger, and U. Henning Regulatory properties of the pyruvate-dehydrogenase complex from Escherichia coli. Positive and negative cooperativity Eur. J. Biochem. 24 1971 376 384
49. T.C. Linn, F.H. Pettit, and L.J. Reed Alpha-keto acid dehydrogenase complexes. X. Regulation of the activity of the pyruvate dehydrogenase complex from beef kidney mitochondria by phosphorylation and dephosphorylation Proc. Natl Acad. Sci. USA 62 1969 234 241
50. O.H. Wieland The mammalian pyruvate dehydrogenase complex: structure and regulation Rev. Physiol. Biochem. Pharmacol. 96 1983 123 170
51. H.C. Su, C.A. Hutchison 3rd, and M.C. Giddings Mapping phosphoproteins in Mycoplasma genitalium and Mycoplasma pneumoniae BMC Microbiol. 7 2007 63
52. M. Wittekind, J. Reizer, J. Deutscher, M.H. Saier, and R.E. Klevit Common structural changes accompany the functional inactivation of HPr by seryl phosphorylation or by serine to aspartate substitution Biochemistry 28 1989 9908 9912 (Pubitemid 20033671)
53. V. Norris, T. den Blaauwen, R.H. Doi, R.M. Harshey, L. Janniere, A. Jimenez-Sanchez, D.J. Jin, P.A. Levin, E. Mileykovskaya, A. Minsky, G. Misevic, C. Ripoll, M. Saier Jr., K. Skarstad, and M. Thellier Toward a hyperstructure taxonomy Annu. Rev. Microbiol. 61 2007 309 329 (Pubitemid 350058211)
54. V. Norris, S. Alexandre, Y. Bouligand, D. Cellier, M. Demarty, G. Grehan, G. Gouesbet, J. Guespin, E. Insinna, L. Le Sceller, B. Maheu, C. Monnier, N. Grant, T. Onoda, N. Orange, A. Oshima, L. Picton, H. Polaert, C. Ripoll, M. Thellier, J.M. Valleton, M.C. Verdus, J.C. Vincent, G. White, and P. Wiggins Hypothesis: hyperstructures regulate bacterial structure and the cell cycle Biochimie 81 1999 915 920 (Pubitemid 29520619)
55. F. Velázquez, K. Pflüger, I. Cases, L.I. De Eugenio, and V. de Lorenzo The phosphotransferase system formed by PtsP, PtsO, and PtsN proteins controls production of polyhydroxyalkanoates in Pseudomonas putida J. Bacteriol. 189 2007 4529 4533 (Pubitemid 46919641)
56. O. Kotte, J.B. Zaugg, and M. Heinemann Bacterial adaptation through distributed sensing of metabolic fluxes Mol. Syst. Biol. 6 2010 355
57. S.S. Mande, S. Sarfaty, M.D. Allen, R.N. Perham, and W.G. Hol Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase Structure 4 1996 277 286
58. G. Burns, P.J. Sykes, K. Hatter, and J.R. Sokatch Isolation of a third lipoamide dehydrogenase from Pseudomonas putida J. Bacteriol. 171 1989 665 668
59. A. Mattevi, G. Obmolova, J.R. Sokatch, C. Betzel, and W.G. Hol The refined crystal structure of Pseudomonas putida lipoamide dehydrogenase complexed with NAD+ at 2.45 A resolution Proteins 13 1992 336 351
60. J.A. Palmer, K.T. Madhusudhan, K. Hatter, and J.R. Sokatch Cloning, sequence and transcriptional analysis of the structural gene for LPD-3, the third lipoamide dehydrogenase of Pseudomonas putida Eur. J. Biochem. 202 1991 231 240
61. J.R. Sokatch, V. McCully, J. Gebrosky, and D.J. Sokatch Isolation of a specific lipoamide dehydrogenase for a branched-chain keto acid dehydrogenase from Pseudomonas putida J. Bacteriol. 148 1981 639 646 (Pubitemid 12218769)
62. J.R. Sokatch, V. McCully, and C.M. Roberts Purification of a branched-chain keto acid dehydrogenase from Pseudomonas putida J. Bacteriol. 148 1981 647 652 (Pubitemid 12218770)
63. K. Regnstrom, S. Sauge-Merle, K. Chen, and B.K. Burgess In Azotobacter vinelandii, the E1 subunit of the pyruvate dehydrogenase complex binds fpr promoter region DNA and ferredoxin I Proc. Natl Acad. Sci. USA 96 1999 12389 12393 (Pubitemid 29513512)
64. B.S. Park, Y.M. Kwon, R. Pyla, J.A. Boyle, and Y.S. Jung E1 component of pyruvate dehydrogenase complex does not regulate the expression of NADPH-ferredoxin reductase in Azotobacter vinelandii FEMS Microbiol. Lett. 273 2007 244 252 (Pubitemid 47084013)
65. M. Butala, S.J. Busby, and D.J. Lee DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes Nucleic Acids Res. 37 2009 e37
66. S. Kale, and F. Jordan Conformational ensemble modulates cooperativity in the rate-determining catalyticttep in the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex J. Biol. Chem. 284 2009 33122 33129
67. S. Kale, G. Ulas, J. Song, G.W. Brudvig, W. Furey, and F. Jordan Efficient coupling of catalysis and dynamics in the E1 component of Escherichia coli pyruvate dehydrogenase multienzyme complex Proc. Natl Acad. Sci. USA 105 2008 1158 1163 (Pubitemid 351397023)
68. M.S. Patel, and L.G. Korotchkina Regulation of the pyruvate dehydrogenase complex Biochem. Soc. Trans. 34 2006 217 222
69. C.G. Mitchell Identification of a multienzyme complex of the tricarboxylic acid cycle enzymes containing citrate synthase isoenzymes from Pseudomonas aeruginosa Biochem. J. 313 Pt 3 1996 769 774 (Pubitemid 26050806)
70. H.V. Patel, K.A. Vyas, X. Li, R. Savtchenko, and S. Roseman Subcellular distribution of enzyme I of the Escherichia coli phosphoenolpyruvate:glycose phosphotransferase system depends on growth conditions Proc. Natl Acad. Sci. USA 101 2004 17486 17491 (Pubitemid 39662756)
71. B. Zimmer, A. Hillmann, and B. Görke Requirements for the phosphorylation of the Escherichia coli EIIANtr protein in vivo FEMS Microbiol. Lett. 286 2008 96 102 (Pubitemid 352040399)
72. J. Puchalka, M.A. Oberhardt, M. Godinho, A. Bielecka, D. Regenhardt, K.N. Timmis, J.A. Papin, and V.A. Martins dos Santos Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology PLoS Comput. Biol. 4 2008 e1000210