Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344

Environmental Microbiology

Volumn 15, Issue 1, 2013, Pages 253-270

  Luque Almagro, Víctor M ^a   Acera, Felipe ^b   Igeño, Ma Isabel ^b   Wibberg, Daniel ^c   Roldán, Ma Dolores ^a   Sáez, Lara P ^a   Hennig, Magdalena ^c   Quesada, Alberto ^b   Huertas, Ma José ^a   Blom, Jochen ^c   Merchán, Faustino ^b   Escribano, Ma Paz ^a   Jaenicke, Sebastian ^c   Estepa, Jessica ^a   Guijo, Ma Isabel ^b   Martínez Luque, Manuel ^a   Macías, Daniel ^b   Szczepanowski, Rafael ^c   Becerra, Gracia ^b   Ramirez, Silvia ^a   Carmona, Ma Isabel ^b   Gutiérrez, Oscar ^a   Manso, Isabel ^a   Pühler, Alfred ^c   Castillo, Francisco ^a   Moreno Vivián, Conrado ^a   Schlüter, Andreas ^c   Blasco, Rafael ^b   more..

^a UNIVERSITY OF CÓRDOBA   (Spain)

^b UNIVERSITY OF EXTREMADURA   (Spain)

^c BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CYANIDE; CYANIDE OXIDASE; HYDROLASE; MIXED FUNCTION OXIDASE; NITRILASE; POLYHYDROXYALKANOIC ACID;

AEROBIC METABOLISM; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; CHEMISTRY; CLASSIFICATION; DNA BASE COMPOSITION; ENZYMOLOGY; GENE ORDER; GENETICS; GENOME SIZE; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PSEUDOMONAS PSEUDOALCALIGENES; SYNTENY;

AEROBIOSIS; AMINO ACID SEQUENCE; AMINOHYDROLASES; BASE COMPOSITION; CYANIDES; GENE ORDER; GENOME SIZE; GENOME, BACTERIAL; MIXED FUNCTION OXYGENASES; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYHYDROXYALKANOATES; PSEUDOMONAS PSEUDOALCALIGENES; SYNTENY;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PSEUDOMONADACEAE; PSEUDOMONAS PSEUDOALCALIGENES;

EID: 84871938416     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2012.02875.x     Document Type: Article

References (74)

1. Alexander, M. (1965) Biodegradation: problems of molecular recalcitrance and microbial fallibility. In Advances in Applied Microbiology. Wayne, W.U. (ed.). New York, USA: Academic Press, pp. 35-80.
2. Allen, S.A., Clark, W., McCaffery, J.M., Cai, Z., Lanctot, A., Slininger, P.J., etal. (2010) Furfural induces reactive oxygen species accumulation and cellular damage in Saccharomyces cerevisiae. Biotechnol Biofuels 3: 2.
3. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
4. Anderson, A.J., and Dawes, E.A. (1990) Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Mol Biol Rev 54: 450-472.
5. Aoyagi, Y., Doi, Y., and Iwata, T. (2003) Mechanical properties and highly ordered structure of ultra-high-molecular-weight poly[(R)-3-hydroxybutyrate] films: effects of annealing and two-step drawing. Polym Degrad Staby 79: 209-216.
6. Arai, H. (2011) Regulation and function of versatile aerobic and anaerobic respiratory metabolism in Pseudomonas aeruginosa. Front Microbiol 2: 1-13.
7. Becerra, G., Blasco, R., Quesada, A., Merchan, F., and Igeño, M.I. (2011) Role of Fur on cyanide tolerance of Pseudomonas pseudoalcaligenes CECT5344. Biochem Soc Trans 39: 1854-1858.
8. Blom, J., Albaum, S., Doppmeier, D., Puhler, A., Vorholter, F.-J., Zakrzewski, M., and Goesmann, A. (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 10: 154.
9. Bork, P., and Koonin, E.V. (1994) A new family of carbon-nitrogen hydrolases. Protein Sci 3: 1344-1346.
10. Carver, T.J., Rutherford, K.M., Berriman, M., Rajandream, M.A., Barrell, B.G., and Parkhill, J. (2005) ACT: the Artemis Comparison Tool. Bioinformatics 21: 3422-3423.
11. Cipollone, R., Ascenzi, P., Tomao, P., Imperi, F., and Visca, P. (2008) Enzymatic detoxification of cyanide: clues from Pseudomonas aeruginosa Rhodanese. J Mol Microbiol Biotechnol 15: 199-211.
12. Cunningham, L., Pitt, M., and Williams, H.D. (1997) The cioAB genes from Pseudomonas aeruginosa code for a novel cyanide-insensitive terminal oxidase related to the cytochrome bd quinol oxidases. Mol Microbiol 24: 579-591.
13. Dhungana, S., Anthony, C.R., 3rd, and Hersman, L.E. (2007) Effect of exogenous reductant on growth and iron mobilization from ferrihydrite by the Pseudomonas mendocina ymp strain. Appl Environ Microbiol 73: 3428-3430.
14. Eikmeyer, F., Hadiati, A., Szczepanowski, R., Wibberg, D., Schneiker-Bekel, S., Rogers, L.M., etal. (2012) The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution. Plasmid 68: 13-24.
15. Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
16. Felsenstein, J. (1995) PHYLIP (Phylogeny Inference Package) Version 3.57c. Seattle, WA, USA: Department of Genetics, University of Washington.
17. Harris, R., and Knowles, C.J. (1983) Isolation and growth of a Pseudomonas Species that utilizes cyanide as a source of nitrogen. J Gen Microbiol 129: 1005-1011.
18. Hedlund, B.P., Geiselbrecht, A.D., and Staley, J.T. (2001) Marinobacter strain NCE312 has a Pseudomonas-like naphthalene dioxygenase. FEMS Microbiol Lett 201: 47-51.
19. Heinl, S., Wibberg, D., Eikmeyer, F., Szczepanowski, R., Blom, J., Linke, B., etal. (2012) Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage. J Biotechnol 161: 153-166.
20. Huertas, M.J., Sáez, L.P., Roldán, M.D., Luque-Almagro, V.M., Martínez-Luque, M., Blasco, R., etal. (2010) Alkaline cyanide degradation by Pseudomonas pseudoalcaligenes CECT5344 in a batch reactor. Influence of pH. J Hazard Mater 179: 72-78.
21. Husemann, P., and Stoye, J. (2010) r2cat: synteny plots and comparative assembly. Bioinformatics 26: 570-571.
22. Igeño, M.I., Becerra, G., Guijo, M.I., Merchan, F., and Blasco, R. (2011) Metabolic adaptation of Pseudomonas pseudoalcaligenes CECT5344 to cyanide: role of malate-quinone oxidoreductases, aconitase and fumarase isoenzymes. Biochem Soc Trans 39: 1849-1853.
23. Iwata, T., Tsunoda, K., Aoyagi, Y., Kusaka, S., Yonezawa, N., and Doi, Y. (2003) Mechanical properties of uniaxially cold-drawn films of poly([R]-3-hydroxybutyrate). Polym Degrad Staby 79: 217-224.
24. Jendrossek, D., and Handrick, R. (2002) Microbial degradation of polyhydroxyalkanoates. Annu Rev Microbiol 56: 403-432.
25. Jiménez, J.I., Miñambres, B., García, J.L., and Díaz, E. (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4: 824-841.
26. Jones, D.T., Taylor, W.R., and Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8: 275-282.
27. Jünemann, S. (1997) Cytochrome bd terminal oxidase. Biochim Biophys Acta 1321: 107-127.
28. Kawakami, T., Kuroki, M., Ishii, M., Igarashi, Y., and Arai, H. (2009) Differential expression of multiple terminal oxidases for aerobic respiration in Pseudomonas aeruginosa. Environ Microbiol 12: 1399-1412.
29. Koopman, F., Wierckx, N., de Winde, J.H., and Ruijssenaars, H.J. (2010) Identification and characterization of the furfural and 5-(hydroxymethyl)furfural degradation pathways of Cupriavidus basilensis HMF14. Proc Natl Acad Sci USA 107: 4919-4924.
30. Kraus, L.M., and Kraus, A.P., Jr (1998) The search for the uremic toxin: the case for carbamoylation of amino acids and proteins. Wien Klin Wochenschr 110: 521-530.
31. Leij, F.R.v.d., and Witholt, B. (1995) Strategies for the sustainable production of new biodegradable polyesters in plants: a review. Can J Microbiol 41: 222-238.
32. Lopez, M.J., Nichols, N.N., Dien, B.S., Moreno, J., and Bothast, R.J. (2004) Isolation of microorganisms for biological detoxification of lignocellulosic hydrolysates. Appl Microbiol Biotechnol 64: 125-131.
33. Luengo, J.M., Garcia, B., Sandoval, A., Naharro, G., and Olivera, E.R. (2003) Bioplastics from microorganisms. Curr Opin Microbiol 6: 251-260.
34. Luque-Almagro, V.M., Blasco, R., Fernandez-Romero, J.M., and de Castro, M.D. (2003) Flow-injection spectrophotometric determination of cyanate in bioremediation processes by use of immobilised inducible cyanase. Anal Bioanal Chem 377: 1071-1078.
35. Luque-Almagro, V.M., Huertas, M.J., Martinez-Luque, M., Moreno-Vivian, C., Roldan, M.D., Garcia-Gil, L.J., etal. (2005) Bacterial degradation of cyanide and its metal complexes under alkaline conditions. Appl Environ Microbiol 71: 940-947.
36. Luque-Almagro, V.M., Huertas, M.J., Roldan, M.D., Moreno-Vivian, C., Martinez-Luque, M., Blasco, R., and Castillo, F. (2007) The cyanotrophic bacterium Pseudomonas pseudoalcaligenes CECT5344 responds to cyanide by defence mechanisms against iron deprivation, oxidative damage and nitrogen stress. Environ Microbiol 9: 1541-1549.
37. Luque-Almagro, V.M., Huertas, M.J., Saez, L.P., Luque-Romero, M.M., Moreno-Vivian, C., Castillo, F., etal. (2008) Characterization of the Pseudomonas pseudoalcaligenes CECT5344 Cyanase, an enzyme that is not essential for cyanide assimilation. Appl Environ Microbiol 74: 6280-6288.
38. Luque-Almagro, V.M., Merchan, F., Blasco, R., Igeño, M.I., Martinez-Luque, M., Moreno-Vivian, C., etal. (2011) Cyanide degradation by Pseudomonas pseudoalcaligenes CECT5344 involves a malate: quinone oxidoreductase and an associated cyanide-insensitive electron transfer chain. Microbiology 157: 739-746.
39. Madison, L.L., and Huisman, G.W. (1999) Metabolic engineering of poly(3-Hydroxyalkanoates): from DNA to plastic. Microbiol Mol Biol Rev 63: 21-53.
40. Martinez, B., Tomkins, J., Wackett, L.P., Wing, R., and Sadowsky, M.J. (2001) Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol 183: 5684-5697.
41. Matsusaki, H., Manji, S., Taguchi, K., Kato, M., Fukui, T., and Doi, Y. (1998) Cloning and molecular analysis of the poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) biosynthesis genes in Pseudomonas sp. strain 61-3. J Bacteriol 180: 6459-6467.
42. Matsusaki, H., Abe, H., and Doi, Y. (2000) Biosynthesis and properties of poly(3-hydroxybutyrate-co-3-hydroxyalkanoates) by recombinant strains of Pseudomonas sp. 61-3. Biomacromolecules 1: 17-22.
43. Meyer, F., Goesmann, A., McHardy, A.C., Bartels, D., Bekel, T., Clausen, J., etal. (2003) GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31: 2187-2195.
44. Nichols, N.N., and Mertens, J.A. (2008) Identification and transcriptional profiling of Pseudomonas putida genes involved in furoic acid metabolism. FEMS Microbiol Lett 284: 52-57.
45. Nogales, J., Canales, Á., Jiménez-Barbero, J., García, J.L., and Díaz, E. (2005) Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440. J Biol Chem 280: 35382-35390.
46. Nogales, J., Canales, A., Jimenez-Barbero, J., Serra, B., Pingarron, J.M., Garcia, J.L., and Diaz, E. (2011) Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol Microbiol 79: 359-374.
47. Oró, J., and Kimball, A.P. (1961) Synthesis of purines under possible primitive earth conditions. I. Adenine from hydrogen cyanide. Arch Biochem Biophys 94: 217-227.
48. Pace, H., and Brenner, C. (2001) The nitrilase superfamily: classification, structure and function. Genome Biol 2: 1-9.
49. Peix, A., Ramirez-Bahena, M.H., and Velazquez, E. (2009) Historical evolution and current status of the taxonomy of genus Pseudomonas. Infect Genet Evol 9: 1132-1147.
50. Piotrowski, M., Schönfelder, S., and Weiler, E.W. (2001) The Arabidopsis thaliana isogene NIT4 and its orthologs in tobacco encode β-cyano-l-alanine hydratase/nitrilase. J Biol Chem 276: 2616-2621.
51. Pitcher, R.S., and Watmough, N.J. (2004) The bacterial cytochrome cbb3 oxidases. Biochim Biophys Acta 1655: 388-399.
52. Pittman, M.S., Robinson, H.C., and Poole, R.K. (2005) A bacterial glutathione transporter (Escherichia coli CydDC) exports reductant to the periplasm. J Biol Chem 280: 32254-32261.
53. Podar, M., Eads, J., and Richardson, T. (2005) Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study. BMC Evol Biol 5: 42.
54. Prieto, M.A., Eugenio, L.I., Galán, B., Luengo, J.M., and Witholt, B. (2007) Synthesis and degradation of polyhydroxyalkanoates. In Pseudomonas. Ramos, J.-L., and Filloux, A. (eds). New York, USA: Springer, pp. 397-428.
55. Quesada, A., Guijo, M.I., Merchan, F., Blazquez, B., Igeño, M.I., and Blasco, R. (2007) Essential role of cytochrome bd-related oxidase in cyanide resistance of Pseudomonas pseudoalcaligenes CECT5344. Appl Environ Microbiol 73: 5118-5124.
56. Ralebits, T.K., Senior, E., and van Verseveld, H.W. (2002) Microbial aspects of atrazine degradation in natural environments. Biodegradation 13: 11-19.
57. Rehm, B.H. (2003) Polyester synthases: natural catalysts for plastics. Biochem J 376: 15-33.
58. Rehm, B.H., and Steinbuchel, A. (1999) Biochemical and genetic analysis of PHA synthases and other proteins required for PHA synthesis. Int J Biol Macromol 25: 3-19.
59. Richardson, D.J. (2000) Bacterial respiration: a flexible process for a changing environment. Microbiology 146: 551-571.
60. Robertson, D.E., Chaplin, J.A., DeSantis, G., Podar, M., Madden, M., Chi, E., etal. (2004) Exploring nitrilase sequence space for enantioselective catalysis. Appl Environ Microbiol 70: 2429-2436.
61. Schneiker-Bekel, S., Wibberg, D., Bekel, T., Blom, J., Linke, B., Neuweger, H., etal. (2011) The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S.meliloti pan-genome. J Biotechnol 155: 20-33.
62. Soldan, P., Pavonic, M., Boucek, J., and Kokes, J. (2001) Baia Mare accident - brief ecotoxicological report of Czech experts. Ecotoxicol Environ Saf 49: 255-261.
63. de Souza, M.L., Seffernick, J., Martinez, B., Sadowsky, M.J., and Wackett, L.P. (1998) The atrazine catabolism genes atzABC are widespread and highly conserved. J Bacteriol 180: 1951-1954.
64. Sudesh, K., Abe, H., and Doi, Y. (2000) Synthesis, structure and properties of polyhydroxyalkanoates: biological polyesters. Prog Polym Sci 25: 1503-1555.
65. Szczepanowski, R., Eikmeyer, F., Harfmann, J., Blom, J., Rogers, L.M., Top, E.M., and Schluter, A. (2011) Sequencing and comparative analysis of IncP-1α antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions. J Biotechnol 155: 95-103.
66. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
67. Timm, A., and Steinbuchel, A. (1990) Formation of polyesters consisting of medium-chain-length 3-hydroxyalkanoic acids from gluconate by Pseudomonas aeruginosa and other fluorescent pseudomonads. Appl Environ Microbiol 56: 3360-3367.
68. Tyagi, M., da Fonseca, M., and de Carvalho, C. (2011) Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes. Biodegradation 22: 231-241.
69. Ugidos, A., Morales, G., Rial, E., Williams, H.D., and Rojo, F. (2008) The coordinate regulation of multiple terminal oxidases by the Pseudomonas putida ANR global regulator. Environ Microbiol 10: 1690-1702.
70. Van der Meer, J.R. (2008) A genomic view on the evolution of catabolic pathways and bacterial adaptation to xenobiotic compounds. In Microbial Biodegradation: Genomics and Molecular Biology. Díaz, E. (ed.). Norfolk, UK: Caister Academic Press, pp. 219-267.
71. Watanabe, A., Yano, K., Ikebukuro, K., and Karube, I. (1998) Cyanide hydrolysis in a cyanide-degrading bacterium, Pseudomonas stutzeri AK61, by cyanidase. Microbiology 144: 1677-1682.
72. Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., etal. (2011) Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. J Biotechnol 155: 50-62.
73. Wierckx, N., Koopman, F., Ruijssenaars, H., and de Winde, J. (2011) Microbial degradation of furanic compounds: biochemistry, genetics, and impact. Appl Microbiol Biotechnol 92: 1095-1105.
74. Yamamoto, S., Kasai, H., Arnold, D.L., Jackson, R.W., Vivian, A., and Harayama, S. (2000) Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146: 2385-2394.