The origin and ecological significance of multiple branches for histidine utilization in Pseudomonas aeruginosa PAO1

Environmental Microbiology

Volumn 14, Issue 8, 2012, Pages 1929-1940

  Gerth, Monica L ^a   Ferla, Matteo P ^b   Rainey, Paul B ^a,c  

^a New Zealand Institute for Advanced Study   (New Zealand)

^b MASSEY UNIVERSITY   (New Zealand)

^c MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

FORMIMINOGLUTAMIC ACID; GLUTAMIC ACID; HISTIDINE;

ARTICLE; BACTERIAL GENOME; BIOSYNTHESIS; CLASSIFICATION; ENVIRONMENT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MUTATION; OPERON; PHYLOGENY; PSEUDOMONAS AERUGINOSA;

ENVIRONMENT; FORMIMINOGLUTAMIC ACID; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; GLUTAMIC ACID; HISTIDINE; MUTATION; OPERON; PHYLOGENY; PSEUDOMONAS AERUGINOSA;

PSEUDOMONAS; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS FLUORESCENS; PSEUDOMONAS FLUORESCENS PF-5; RALSTONIA;

EID: 84864384632     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2011.02691.x     Document Type: Article

References (69)

1. Alvarez-Ortega, C., and Harwood, C.S. (2007) Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration. Mol Microbiol 65: 153-165.
2. Bazurto, J.V., and Downs, D.M. (2011) Plasticity in the purine-thiamine metabolic network of Salmonella. Genetics 187: 623-631.
3. Beasley, J.E., and Planes, F.J. (2007) Recovering metabolic pathways via optimization. Bioinformatics 23: 92-98.
4. Berg, O.G., and Kurland, C.G. (2002) Evolution of microbial genomes: sequence acquisition and loss. Mol Biol Evol 19: 2265-2276.
5. Bochner, B.R., and Savageau, M.A. (1979) Inhibition of growth by imidazol(on)e propionic acid: evidence in vivo for coordination of histidine catabolism with the catabolism of other amino acids. Mol Gen Genet 168: 87-95.
6. Boulette, M.L., Baynham, P.J., Jorth, P.A., Kukavica-Ibrulj, I., Longoria, A., Barrera, K., etal. (2009) Characterization of alanine catabolism in Pseudomonas aeruginosa and its importance for proliferation in vivo. J Bacteriol 191: 6329-6334.
7. Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540-552.
8. Choi, K.H., and Schweizer, H.P. (2006) mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa. Nat Protoc 1: 153-161.
9. Clarke, P.H. (1969) The aliphatic amidases of Pseudomonas aeruginosa. In Advances in Microbial Physiology. Rose, A.H., and Wilkinson, J.F. (eds). New York, USA: Academic press Inc., pp. 179-222.
10. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., etal. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
11. Dam, P., Olman, V., Harris, K., Su, Z., and Xu, Y. (2007) Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res 35: 288-298.
12. Dean, E.J., Davis, J.C., Davis, R.W., and Petrov, D.A. (2008) Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet 4: e1000113.
13. Denef, V.J., Klappenbach, J.A., Patrauchan, M.A., Florizone, C., Rodrigues, J.L.M., Tsoi, T.V., etal. (2006) Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Appl Environ Microbiol 72: 585-595.
14. Ditta, G., Stanfield, S., Corbin, D., and Helinski, D.R. (1980) Broad host range DNA cloning system for gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc Natl Acad Sci USA 77: 7347-7351.
15. Edelman, G.M., and Gally, J.A. (2001) Degeneracy and complexity in biological systems. Proc Natl Acad Sci USA 98: 13763-13768.
16. Fung, C., Naughton, S., Turnbull, L., Tingpej, P., Rose, B., Arthur, J., etal. (2010) Gene expression of Pseudomonas aeruginosa in a mucin-containing synthetic growth medium mimicking cystic fibrosis lung sputum. J Med Microbiol 59: 1089-1100.
17. Gu, Z., Steinmetz, L.M., Gu, X., Scharfe, C., Davis, R.W., and Li, W.H. (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63-66.
18. Harrison, R., Papp, B., Pal, C., Oliver, S.G., and Delneri, D. (2007) Plasticity of genetic interactions in metabolic networks of yeast. Proc Natl Acad Sci USA 104: 2307-2312.
19. Heckman, K.L., and Pease, L.R. (2007) Gene splicing and mutagenesis by PCR-driven overlap extension. Nat Protoc 2: 924-932.
20. Helling, R.B. (1994) Why does Escherichia coli have two primary pathways for synthesis of glutamate? J Bacteriol 176: 4664-4668.
21. Hu, L., and Phillips, A.T. (1988) Organization and multiple regulation of histidine utilization genes in Pseudomonas putida. J Bacteriol 170: 4272-4279.
22. Hu, L., Mulfinger, L.M., and Phillips, A.T. (1987) Purification and properties of formylglutamate amidohydrolase from Pseudomonas putida. J Bacteriol 169: 4696-4702.
23. Itoh, Y., Nighijyo, T., and Nakada, Y. (2007) Histidine catabolism and catabolite regulation. Pseudomonas 6: 371-395.
24. Johnson, D.A., Tetu, S.G., Phillippy, K., Chen, J., Ren, Q., and Paulsen, I.T. (2008) High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes. PLoS Genet 4: e1000211.
25. Kaminskas, E., Kimhi, Y., and Magasanik, B. (1970) Urocanase and N-formimino-l-glutamate formiminohydrolase of Bacillus subtilis, two enzymes of the histidine degradation pathway. J Biol Chem 245: 3536-3544.
26. Kelly, M., and Clarke, P.H. (1962) An inducible amidase produced by a strain of Pseudomonas aeruginosa. J Gen Microbiol 27: 305-316.
27. Kimhi, Y., and Magasanik, B. (1970) Genetic basis of histidine degradation in Bacillus subtilis. J Biol Chem 245: 3545-3548.
28. Krell, T., Molina-Henares, A.J., and Ramos, J.L. (2006) The IclR family of transcriptional activators and repressors can be defined by a single profile. Protein Sci 15: 1207-1213.
29. Kwon, D.H., and Lu, C.D. (2006) Polyamines induce resistance to cationic peptide, aminoglycoside, and quinolone antibiotics in Pseudomonas aeruginosa PAO1. Antimicrob Agents Chemother 50: 1615-1622.
30. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., etal. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
31. Lenski, R.E., Rose, M.R., Simpson, S.C., and Tadler, S.C. (1991) Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2000 generations. Am Nat 138: 1315.
32. Lessie, T.G., and Neidhardt, F.C. (1967) Formation and operation of the histidine-degrading pathway in Pseudomonas aeruginosa. J Bacteriol 93: 1800-1810.
33. Letunic, I., and Bork, P. (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: W475-W478.
34. Lind, P.A., Tobin, C., Berg, O.G., Kurland, C.G., and Andersson, D.I. (2010) Compensatory gene amplification restores fitness after inter-species gene replacements. Mol Microbiol 75: 1078-1089.
35. Magasanik, B., Lund, P., Neidhardt, F.C., and Schwartz, D.T. (1965) Induction and repression of the histidine-degrading enzymes in Aerobacter aerogenes. J Biol Chem 240: 4320-4324.
36. Mahadevan, R., and Lovley, D.R. (2008) The degree of redundancy in metabolic genes is linked to mode of metabolism. Biophys J 94: 1216-1220.
37. Marti-Arbona, R., Xu, C., Steele, S., Weeks, A., Kuty, G.F., Seibert, C.M., and Raushel, F.M. (2006) Annotating enzymes of unknown function: N-formimino-l-glutamate deiminase is a member of the amidohydrolase superfamily. Biochemistry 45: 1997-2005.
38. Marx, C.J., Miller, J.A., Chistoserdova, L., and Lidstrom, M.E. (2004) Multiple formaldehyde oxidation/detoxification pathways in Burkholderia fungorum LB400. J Bacteriol 186: 2173-2178.
39. Mashburn, L.M., Jett, A.M., Akins, D.R., and Whiteley, M. (2005) Staphylococcus aureus serves as an iron source for Pseudomonas aeruginosa during in vivo coculture. J Bacteriol 187: 554-566.
40. Meléndez-Hevia, E., Waddell, T.G., and Montero, F. (1994) Optimization of metabolism: the evolution of metabolic pathways toward simplicity through the game of the pentose phosphate cycle. J Theor Biol 166: 201-220.
41. Mendonça, A.G., Alves, R.J., and Pereira-Leal, J.B. (2011) Loss of genetic redundancy in reductive genome evolution. PLoS Comput Biol 7: e1001082.
42. Molina-Henares, A.J., Krell, T., Eugenia Guazzaroni, M., Segura, A., and Ramos, J.L. (2006) Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors. FEMS Microbiol Rev 30: 157-186.
43. Musken, M., Di Fiore, S., Dotsch, A., Fischer, R., and Haussler, S. (2010) Genetic determinants of Pseudomonas aeruginosa biofilm establishment. Microbiology 156: 431-441.
44. Neidhardt, F.C., and Magasanik, B. (1957) Reversal of the glucose inhibition of histidase biosynthesis in Aerobacter aerogenes. J Bacteriol 73: 253-259.
45. Ochman, H., Lawrence, J.G., and Groisman, E.A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
46. Pal, C., Papp, B., and Lercher, M.J. (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37: 1372-1375.
47. Palmer, K.L., Aye, L.M., and Whiteley, M. (2007) Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum. J Bacteriol 189: 8079-8087.
48. Papp, B., Teusink, B., and Notebaart, R.A. (2009) A critical view of metabolic network adaptations. HFSP J 3: 24-35.
49. Patell, S., Gu, M., Davenport, P., Givskov, M., Waite, R.D., and Welch, M. (2010) Comparative microarray analysis reveals that the core biofilm-associated transcriptome of Pseudomonas aeruginosa comprises relatively few genes. Environ Microbiol Rep 2: 440-448.
50. Rainey, P.B. (1999) Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1: 243-257.
51. Rediers, H., Vanderleyden, J., and De Mot, R. (2004) Azotobacter vinelandii: a Pseudomonas in disguise? Microbiology 150: 1117-1119.
52. Reese, M.G. (2001) Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 26: 51-56.
53. Rietsch, A., Wolfgang, M.C., and Mekalanos, J.J. (2004) Effect of metabolic imbalance on expression of type III secretion genes in Pseudomonas aeruginosa. Infect Immun 72: 1383-1390.
54. Rodriguez, R.L., and West, R.W., Jr (1984) Histidine operon control region of Klebsiella pneumoniae: analysis with an Escherichia coli promoter-probe plasmid vector. J Bacteriol 157: 764-771.
55. Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., etal. (2010) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 38: D5-D16.
56. Smith, G.R., Halpern, Y.S., and Magasanik, B. (1971) Genetic and metabolic control of enzymes responsible for histidine degradation in Salmonella typhimurium. J Biol Chem 246: 3320-3329.
57. Soyer, O.S., and Pfeiffer, T. (2010) Evolution under fluctuating environments explains observed robustness in metabolic networks. PLoS Comput Biol 6: e1000907.
58. Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
59. Stover, C.K., Pham, X.Q., Erwin, A.L., Mizoguchi, S.D., Warrener, P., Hickey, M.J., etal. (2000) Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406: 959-964.
60. Tabor, H., and Mehler, A.H. (1954) Isolation of N-formyl-l-glutamic acid as an intermediate in the enzymatic degradation of l-histidine. J Biol Chem 210: 559-568.
61. Thompson, I.P., Lilley, A.K., Ellis, R.J., Bramwell, P.A., and Bailey, M.J. (1995) Survival, colonization and dispersal of genetically modified Pseudomonas fluorescens SBW25 in the phytosphere of field grown sugar beet. Nat Biotechnol 13: 1493-1497.
62. Velayudhan, J., Jones, M.A., Barrow, P.A., and Kelly, D.J. (2004) l-Serine catabolism via an oxygen-labile l-Serine dehydratase is essential for colonization of the avian gut by Campylobacter jejuni. Infect Immun 72: 260-268.
63. Whitacre, J., and Bender, A. (2010) Degeneracy: a design principle for achieving robustness and evolvability. J Theor Biol 263: 143-153.
64. Williams, K.P., Gillespie, J.J., Sobral, B.W., Nordberg, E.K., Snyder, E.E., Shallom, J.M., and Dickerman, A.W. (2010) Phylogeny of gammaproteobacteria. J Bacteriol 192: 2305-2314.
65. Winsor, G.L., Van Rossum, T., Lo, R., Khaira, B., Whiteside, M.D., Hancock, R.E.W., and Brinkman, F.S.L. (2009) Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res 37: D483-D488.
66. Yeung, A.T.Y., Torfs, E.C.W., Jamshidi, F., Bains, M., Wiegand, I., Hancock, R.E.W., and Overhage, J. (2009) Swarming of Pseudomonas aeruginosa is controlled by a broad spectrum of transcriptional regulators, including MetR. J Bacteriol 191: 5592-5602.
67. Young, J.M., and Park, D.C. (2007) Probable synonymy of the nitrogen-fixing genus Azotobacter and the genus Pseudomonas. Int J Syst Evol Microbiol 57: 2894-2901.
68. Zhang, X.X., and Rainey, P.B. (2007a) Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25. Genetics 176: 2165-2176.
69. Zhang, X.X., and Rainey, P.B. (2007b) Construction and validation of a neutrally-marked strain of Pseudomonas fluorescens SBW25. J Microbiol Methods 71: 78-81.