Unraveling an FNR based regulatory circuit in Paracoccus denitrificans using a proteomics-based approach

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1804, Issue 6, 2010, Pages 1350-1358

  Bouchal, Pavel ^a   Struhárová, Iva ^a   Budinská, Eva ^a   Šedo, Ondrej ^a   Vyhlídalová, Tereza ^a   Zdráhal, Zbyněk ^a   van Spanning, Rob ^b   Kučera, Igor ^a  

^a MASARYK UNIVERSITY   (Czech Republic)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

FNR transcription regulator; Paracoccus denitrificans; Proteome; Respiratory switch; Two dimensional gel electrophoresis

Indexed keywords

FUMARATE AND NITRATE REDUCTASE REGULATORY PROTEIN; NARR PROTEIN; NITRITE REDUCTASE; NITROUS OXIDE REDUCTASE; NNR PROTEIN; OMPW PROTEIN; PROTEIN; PROTEOME; SODIUM NITRATE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; USPA PROTEIN;

ARTICLE; CONTROLLED STUDY; MASS SPECTROMETRY; NONHUMAN; PARACOCCUS DENITRIFICANS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; REAL TIME POLYMERASE CHAIN REACTION; TWO DIMENSIONAL GEL ELECTROPHORESIS; WILD TYPE;

AEROBIOSIS; ANAEROBIOSIS; BACTERIAL PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; NITRIC OXIDE; NITRITES; OXYGEN; PARACOCCUS DENITRIFICANS; PROTEOMICS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); PARACOCCUS DENITRIFICANS;

EID: 77949917360     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2010.01.016     Document Type: Article

References (31)

1. Zumft W.G. Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61 (1997) 533-616
2. Berks B.C., Ferguson S.J., Moir J.W.B., and Richardson D.J. Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. Biochim. Biophys. Acta 1232 (1995) 97-173
3. Baker S.C., Ferguson S.J., Ludwig B., Page M.D., Richter O.M., and van Spanning R.J.M. Molecular genetics of the genus Paracoccus: metabolically versatile bacteria with bioenergetic flexibility. Microbiol. Mol. Biol. Rev. 62 (1998) 1046-1078
4. Wood N.J., Alizadeh T., Bennett S., Pearce J., Ferguson S.J., Richardson D.J., and Moir J.W. Maximal expression of membrane-bound nitrate reductase in Paracoccus is induced by nitrate via a third FNR-like regulator named NarR. J. Bacteriol. 183 (2001) 3606-3613
5. Van Spanning R.J.M., De Boer A.P.N., Reijnders W.N.M., Westerhoof H.V., Stouthamer A.H., and van der Oost J. FnrP and NNR of Paracoccus denitrificans are both members of the FNR family of transcriptional activators but have distinct roles in respiratory adaptation in response to oxygen limitation. Mol. Microbiol. 12 (1997) 893-907
6. Van Spanning R.J.M., De Boer A.P.N., Reijnders W.N.M., Spiro S., Westerhoof H.V., Stouthamer A.H., and Van der Oost J. Nitrite and nitric oxide reduction in Paracoccus denitrificans is under the control of NNR, a regulatory protein that belongs to the FNR family of transcriptional activators. FEBS Lett. 360 (1995) 151-154
7. Veldman R., Reijnders W.N.M., and van Spanning R.J.M. Specificity of FNR-type regulators in Paracoccus denitrificans. Biochem. Soc. Trans. 34 (2006) 94-96
8. Van Spanning R.J.M., De Boer A.P., Reijnders W.N., Spiro S., Westerhoff H.V., Stouthamer A.H., and Van der Oost J. Nitrite and nitric oxide reduction in Paracoccus denitrificans is under the control of NNR, a regulatory protein that belongs to the FNR family of transcriptional activators. FEBS Lett. 360 (1995) 151-154
9. Bouchal P., Zdrahal Z., Helanova S., Janiczek O., Hallberg K.B., and Mandl M. Proteomic and bioinformatic analysis of iron- and sulfur-oxidizing Acidithiobacillus ferrooxidans using immobilized pH gradients and mass spectrometry. Proteomics 6 (2006) 4278-4285
10. Bouchal P., Precechtelova P., Zdrahal Z., and Kucera I. Protein composition of Paracoccus denitrificans cells grown on various electron acceptors and in the presence of azide. Proteomics 4 (2004) 2662-2671
11. Rabilloud T. A comparison between low background silver diammine and silver nitrate protein stains. Electrophoresis 13 (1992) 429-439
12. Tusher V.G., Tibshirani R., and Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. U. S. A. 98 (2001) 5116-5121
13. R_Development_Core_Team. A Language and Environment for Statistical Computing (2008), R Foundation for Statistical Computing, Vienna, Austria
14. Havlis J., Thomas H., Sebela M., and Shevchenko A. Fast-response proteomics by accelerated in-gel digestion of proteins. Anal. Chem. 75 (2003) 1300-1306
15. Planeta J., Karasek P., and Vejrosta J. Development of packed capillary columns using carbon dioxide slurries. J. Sep. Sci. 26 (2003) 525-530
16. Mazoch J., and Kucera I. Control of gene expression by FNR-like proteins in facultatively anaerobic bacteria. Folia Microbiol. (Praha) 47 (2002) 95-103
17. Lee Y.Y., Shearer N., and Spiro S. Transcription factor NNR from Paracoccus denitrificans is a sensor of both nitric oxide and oxygen: isolation of nnr* alleles encoding effector-independent proteins and evidence for a haem-based sensing mechanism. Microbiology 152 (2006) 1461-1470
18. Kvint K., Nachin L., Diez A., and Nystrom T. The bacterial universal stress protein: function and regulation. Curr. Opin. Microbiol. 6 (2003) 140-145
19. Kao D.Y., Cheng Y.C., Kuo T.Y., Lin S.B., Lin C.C., Chow L.P., and Chen W.J. Salt-responsive outer membrane proteins of Vibrio anguillarum serotype O1 as revealed by comparative proteome analysis. J. Appl. Microbiol. 106 (2009) 2079-2085
20. Neher T.M., and Lueking D.R. Pseudomonas fluorescens ompW: plasmid localization and requirement for naphthalene uptake. Can. J. Microbiol. 55 (2009) 553-563
21. Gil F., Ipinza F., Fuentes J., Pumeron P., Villarreal J.M., Aspee A., Mora G.C., Vasquez C.C., and Saavedra C. The ompW (porin) gene mediates methyl viologen (paraquat) efflux in Salmonella enterica serovar Typhimurium. Res. Microbiol. 158 (2007) 529-536
22. Wu L., Lin X.M., and Peng X.X. From proteome to genome for functional characterization of pH-dependent outer membrane proteins in Escherichia coli. J. Proteome Res. 8 (2009) 1059-1070
23. Gil F., Hernandez-Lucas I., Polanco R., Pacheco N., Collao B., Villarreal J.M., Nardocci G., Calva E., and Saavedra C.P. SoxS regulates the expression of the Salmonella enterica serovar Typhimurium ompW gene. Microbiology 155 (2009) 2490-2497
24. Cornelis P., Matthijs S., and Van Oeffelen L. Iron uptake regulation in Pseudomonas aeruginosa. Biometals 22 (2009) 15-22
25. Schauer K., Rodionov D.A., and de Reuse H. New substrates for TonB-dependent transport: do we only see the 'tip of the iceberg'?. Trends Biochem. Sci. 33 (2008) 330-338
26. Lee H.S., Abdelal A.H., Clark M.A., and Ingraham J.L. Molecular characterization of nosA, a Pseudomonas stutzeri gene encoding an outer membrane protein required to make copper-containing N2O reductase. J. Bacteriol. 173 (1991) 5406-5413
27. Kavanagh K.L., Jornvall H., Persson B., and Oppermann U. Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes. Cell. Mol. Life Sci. 65 (2008) 3895-3906
28. Pang A.S., Nathoo S., and Wong S.L. Cloning and characterization of a pair of novel genes that regulate production of extracellular enzymes in Bacillus subtilis. J. Bacteriol. 173 (1991) 46-54
29. Seshasayee A.S., Bertone P., Fraser G.M., and Luscombe N.M. Transcriptional regulatory networks in bacteria: from input signals to output responses. Curr. Opin. Microbiol. 9 (2006) 511-519
30. Balazsi G., Barabasi A.L., and Oltvai Z.N. Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc. Natl. Acad. Sci U. S. A. 102 (2005) 7841-7846
31. Yamamoto K., Hirao K., Oshima T., Aiba H., Utsumi R., and Ishihama A. Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli. J. Biol. Chem. 280 (2005) 1448-1456