The biotechnological potential of the extreme halophilic archaea Haloterrigena sp. H13 in xenobiotic metabolism using a comparative genomics approach

Environmental Technology

Volumn 31, Issue 8-9, 2010, Pages 905-914

  Ding, Jiun Yan ^a   Lai, Mei Chin ^a  

^a NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

Author keywords

comparative genomics; extremophiles; halophilic archaea; xenobiotic degradation

Indexed keywords

BIOREMEDIATION; BIOTECHNOLOGY; CATALYSTS; ENZYMES; GENES; METABOLISM; NAPHTHALENE; PLANTS (BOTANY);

2-METHYLNAPHTHALENE; ARCHAEON; BIOTECHNOLOGICAL APPLICATIONS; COMPARATIVE GENOMICS; CONTIGS; DEGRADING ENZYMES; DICHLOROETHANE; EXTREMOPHILES; GENOME ANNOTATION; GENOME SIZES; HALOACID DEHALOGENASE; HALOPHILIC ARCHAEA; HEXACHLOROCYCLOHEXANES; HYPERSALINE ENVIRONMENT; METABOLIC PATHWAYS; OPEN READING FRAME; PARTIAL GENOMES; SALICYLATE HYDROXYLASE; XENOBIOTIC METABOLISM;

DEGRADATION;

1 METHYLNAPHTHALENE; 1,2 DICHLOROETHANE; 2 METHYLNAPHTHALENE; ANTHRACENE; BENZOIC ACID; COENZYME A; CONTIG; DICHLOROETHANE; HALOACID; HEXACHLOROCYCLOHEXANE; NAPHTHALENE; SALICYLIC ACID;

BIOREMEDIATION; DEGRADATION; ENZYME ACTIVITY; EXTREMOPHILE; GENE; GENETIC ANALYSIS; GENOMICS; HYPERSALINE ENVIRONMENT; METABOLISM; NAPHTHALENE; PROKARYOTE; XENOBIOTICS;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BIOTECHNOLOGY; COMPARATIVE GENOMIC HYBRIDIZATION; GENE IDENTIFICATION; GENE SEQUENCE; GENOME SIZE; HALOPHILIC ARCHAEON; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; XENOBIOTIC METABOLISM;

ARCHAEA; BACTERIA (MICROORGANISMS); HALOBACTERIA; HALOTERRIGENA;

EID: 77953722893     PISSN: 09593330     EISSN: 1479487X     Source Type: Journal    
DOI: 10.1080/09593331003734210     Document Type: Article

References (53)

1. F. Junker, T. Leisinger, and A.M. Cook, 3-Sulphocatechol 2,3-dioxygenase and other dioxygenases (EC 1.13.11.2 and EC 1.14.12.-) in the degradative pathways of 2-aminobenzenesulphonic, benzenesulphonic and 4-toluenesulphonic acids in Alcaligenes sp. strain O-1, Microbiology 140 (1994), pp. 1713-1722.
2. G. Pandey, D. Paul, and R.K. Jain, Branching of onitrobenzoate degradation pathway in Arthrobacter protophormiae RKJ100: Identification of new intermediates, FEMS Microbiol. Lett. 9 (2003), pp. 231-236.
3. H.R. Beller and A.M. Spormann, Anaerobic activation of toluene and o-xylene by addition to fumarate in denitrifying strain T, J. Bacteriol 179 (1997), pp. 670-676.
4. K. Günther, D. Schlosser, and W. Fritsche, Phenol and cresol metabolism in Bacillus pumilus isolated from contaminated groundwater, J. Basic Microbiol. 35 (1995), pp. 83-92.
5. P.E. Rouvière and M.W. Chen, Isolation of Brachymonas petroleovorans CHX, a novel cyclohexane-degrading beta-proteobacterium, FEMS Microbiol. Lett. 227 (2003), pp. 101-106.
6. S. Takenaka, S. Okugawa, M. Kadowaki, S. Murakami, and K. Aoki, The metabolic pathway of 4-aminophenol in Burkholderia sp. strain AK-5 differs from that of aniline and aniline with C-4 substituents, Appl. Environ. Microbiol. 69 (2003), pp. 5410-5413.
7. Z. He and J. Wiegel, Purification and characterization of an oxygen-sensitive reversible 4-hydroxybenzoate decarboxylase from Clostridium hydroxybenzoicum, Eur. J. Biochem. 229 (1995), pp. 77-82.
8. X. Maymó-Gatell, Y. Chien, J.M. Gossett, and S.H. Zinder, Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene, Science 276 (1997), pp. 1568-1571.
9. S. Blümel, M. Contzen, M. Lutz, A. Stolz, and H.J. Knackmuss, Isolation of a bacterial strain with the ability to utilize the sulfonated azo compound 4- carboxy-4'-sulfoazobenzene as the sole source of carbon and energy, Appl. Environ. Microbiol. 64 (1998), pp. 2315-2317.
10. R. van Herwijnen, D. Springael, P. Slot, H.A. Govers, and J.R. Parsons, Degradation of anthracene by Mycobacterium sp. strain LB501T proceeds via a novel pathway, through o-phthalic acid, Appl. Environ. Microbiol. 69 (2003), pp. 186-190.
11. A.G. Hay and D.D. Focht, Cometabolism of 1,1- dichloro-2,2-bis(4- chlorophenyl)ethylene by Pseudomonas acidovorans M3GY grown on biphenyl, Appl. Environ. Microbiol. 64 (1998), pp. 2141-2146.
12. R.S. Kulkarni and P.P. Kanekar, Bioremediation of epsilon- caprolactam from nylon-6 waste water by use of Pseudomonas aeruginosa MCM B-407, Curr. Microbiol. 37 (1998), pp. 191-194.
13. M.C. Mahajan, P.S. Phale, and C.S. Vaidyanathan, Evidence for the involvement of multiple pathways in the biodegradation of 1- and 2-methylnaphthalene by Pseudomonas putida CSV86, Arch. Microbiol. 161 (1994), pp. 425-433.
14. P.S. Phale, M.C. Mahajan, and C.S. Vaidyanathan, A pathway for biodegradation of 1-naphthoic acid by Pseudomonas maltophilia CSV89, Arch. Microbiol. 163 (1995), pp. 42-47.
15. G.J. Poelarends, M. Wilkens, M.J. Larkin, J.D. van Elsas, and D.B. Janssen, Degradation of 1,3-dichloropropene by Pseudomonas cichorii 170, Appl. Environ. Microbiol. 64 (1998), pp. 2931-2938.
16. M. Seeger, K.N. Timmis, and B. Hofer, Conversion of chlorobiphenyls into phenylhexadienoates and benzoates by the enzymes of the upper pathway for polychlorobiphenyl degradation encoded by the bph locus of Pseudomonas sp. strain LB400, Appl. Envion. Microbiol. 61 (1995), pp. 2654-2658.
17. A.M. Warhurst, K.F. Clarke, R.A. Hill, R.A. Holt, and C.A. Fewson, Metabolism of styrene by Rhodococcus rhodochrous NCIMB 13259, Appl. Environ. Microbiol. 60 (1994), pp. 1137-1145.
18. W. van Doesburg, M.H. van Eekert, P.J. Middeldorp, M. Balk, G. Schraa, and A.J. Stams, Reductive dechlorination of beta-hexachlorocyclohexane (beta- HCH) by a Dehalobacter species in coculture with a Sedimentibacter sp., FEMS Microbiol. Ecol. 54 (2005), pp. 87-95.
19. Y. Nagata, Z. Prokop, Y. Sato, P. Jerabek, A. Kumar, Y. Ohtsubo, M. Tsuda, and J. Damborsky, Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26, Appl. Environ. Microbiol. 71 (2005), pp. 2183-2185.
20. L. Monna, T. Omori, and T. Kodama, Microbial degradation of dibenzofuran, fluorene, and dibenzo-p-dioxin by Staphylococcus auriculans DBF63, Appl. Environ. Microbiol. 59 (1993), pp. 285-289.
21. T. Biegert, G. Fuchs, and J. Heider, Evidence that anaerobic oxidation of toluene in the denitrifying bacterium Thauera aromatica is initiated by formation of benzylsuccinate from toluene and fumarate, Eur. J. Biochem. 238 (1996), pp. 661-668.
22. C. Sommer and H. Görisch, Enzymology of the degradation of (di)chloro-benzenes by Xanthobacter flavus 14p1, Arch. Microbiol. 167 (1997), pp. 384-391. [23]
23. S.H. Zinder, K.R. Sowers, and J.G. Ferry, Methanosarcina thermophila sp. nov., a thermophilic, acetotrophic, methane-producing bacterium, Int. J. Syst. Bacteriol. 35 (1985), pp. 522-523.
24. P.E. Jablonski and J.G. Ferry, Reductive dechlorination of trichloroethylene by the CO-reduced CO dehydrogenase enzyme complex from Methanosarcina thermophila, FEMS Microbiol. Lett. 75 (1992), pp. 55-59.
25. V. Izzo, E. Notomista, A. Picardi, F. Pennacchio, and A. Di Donato, The thermophilic archaeon Sulfolobus solfataricus is able to grow on phenol, Res. Microbiol. 156 (2005), pp. 677-689.
26. D. Emerson, S. Chauhan, P. Oriel, and J.A. Breznak, Haloferax sp. D1227, a halophilic archaeon capable of growth on aromatic compounds, Arch. Microbiol. 161 (1994), pp. 445-452.
27. D.J. Fairley, G. Wang, C. Rensing, I.L. Pepper, and M.J. Larkin, Expression of gentisate 1,2-dioxygenase (gdoA) genes involved in aromatic degradation in two haloarchaeal genera, Appl. Microbiol. Biotechnol. 73 (2006), pp. 691-695.
28. W. Fu and P. Oriel, Degradation of 3-phenylpropionic acid by Haloferax sp. D1227, Extremophiles 3 (1999), pp. 45-53.
29. T.M. Raghavan and I. Furtado, Tolerance of an estuarine halophilic archaebacterium to crude oil and constituent hydrocarbons, Bull. Environ. Contam. Toxicol. 65 (2000), pp. 725-731.
30. I.S. Kulichevskaya, E.I. Milekhina, I.A. Borzenkov, I.S. Zvyagintseva, and S.S. Belyaev, Oxidation of petroleum hydrocarbons by extremely halophilic archaebacteria, Microbiology 60 (1992), pp. 596-601.
31. P.S. Suresh, A. Kumar, R. Kumar, and V.P. Singh, An in silico approach to bioremediation: Laccase as a case study, J. Mol. Graph. Model. 26 (2008), pp. 845-849.
32. C.J. Bult, O. White, G.J. Olsen, L. Zhou, R.D. Fleischmann, G.G. Sutton, J.A. Blake, L.M. FitzGerald, R.A. Clayton, J.D. Gocayne, A.R. Kerlavage, B.A. Dougherty, J.F. Tomb, M.D. Adams, C.I. Reich, R. Overbeek, E.F. Kirkness, K.G. Weinstock, J.M. Merrick, A. Glodek, J.L. Scott, N.S. Geoghagen, and J.C. Venter, Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii, Science 273 (1996), pp. 1058-1073.
33. W.V. Ng, S.P. Kennedy, G.G. Mahairas, B. Berquist, M. Pan, H.D. Shukla, S.R. Lasky, N.S. Baliga, V. Thorsson, J. Sbrogna, S. Swartzell, D. Weir, J. Hall, T.A. Dahl, R. Welti, Y.A. Goo, B. Leithauser, K. Keller, R. Cruz, M.J. Danson, D.W. Hough, D.G. Maddocks, P.E. Jablonski, M.P. Krebs, C.M. Angevine, H. Dale, T.A. Isenbarger, R.F. Peck, M. Pohlschroder, J.L. Spudich, K.W. Jung, M. Alam, T. Freitas, S. Hou, C.J. Daniels, P.P. Dennis, A.D. Omer, H. Ebhardt, T.M. Lowe, P. Liang, M. Riley, L. Hood, and S. DasSarma, Genome sequence of Halobacterium species NRC-1, Proc. Nat. Acad. Sci. U.S.A. 97 (2000), pp. 12176-12181.
34. Y.A. Goo, J. Roach, G. Glusman, N.S. Baliga, K. Deutsch, M. Pan, S. Kennedy, S. DasSarma, W.V. Ng, and L. Hood, Low-pass sequencing for microbial comparative genomics, BMC Genomics 5 (2004), pp. 5-21.
35. M.C. Lai, J.Y. Ding, M.C. Lin, C.C. Kuo, and S.H. Hsu, New halophilic archaea isolated from the solar saltern synthesis novel biodegradable polyester, I-113, 103rd General Meeting of the American Society for Microbiology, Washington, DC, 2003.
36. H. Hackett, Preparation of intact, agarose-embedded DNA from Halobacterium halobium and its digestion by restriction enzyme, in Halophiles, Archaea: A Laboratory Manual, S. DasSarma and E.M. Fleichmann, eds., Cold Spring Harbor Laboratory Press, New York, 1995, pp. 185-187.
37. K.F. Jarrell, D. Faguy, A.M. Hebert, and M.A. Kalmokoff, A general method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria), Can. J. Microbiol. 38 (1992), pp. 65-68.
38. J. Sambrook and D.W. Russell, Molecular Cloning, 3rd ed., Cold Spring Harbor Laboratory Press, New York, 2001.
39. B. Ewing and P. Green, Base-calling of automated sequencer traces using phred. II. Error probabilities, Genome Res. 8 (1998), pp. 186-194.
40. S. Li and H.H. Chou, LUCY2: An interactive DNA sequence quality trimming and vector removal tool, Bioinformatics 20 (2004), pp. 2865-2866.
41. N.S. Baliga, R. Bonneau, M.T. Facciotti, M. Pan, G. Glusman, E.W. Deutsch, P. Shannon, Y. Chiu, R.S. Weng, R.R. Gan, P. Hung, S.V. Date, E. Marcotte, L. Hood, and W.V. Ng, Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea, Genome Res. 14 (2004), pp. 2221-2234.
42. H. Bolhuis, P. Palm, A. Wende, M. Falb, M. Rampp, F. Rodriguez-Valera, F. Pfeiffer, and D. Oesterhelt, The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity, BMC Genomics 7 (2006), p. 169.
43. M. Falb, F. Pfeiffer, P. Palm, K. Rodewald, V. Hickmann, J. Tittor, and D. Oesterhelt, Living with two extremes: Conclusions from the genome sequence of Natronomonas pharaonis, Genome Res. 15 (2005), pp. 1336-1343.
44. S.P. Kennedy, W.V. Ng, S.L. Salzberg, L. Hood, and S. DasSarma, Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence, Genome Res. 11 (2001), pp. 1641-1650.
45. J.H. Do and D.K. Choi, Computational approaches to gene prediction, J. Microbiol. 44 (2006), pp. 137-144.
46. M. Falb, Computational genome and pathway analysis of halophilic archaea, Ph.D. diss., LMU München, 2005.
47. A.V. Akolkar, G.M. Deshpande, K.N. Raval, D. Durai, A.S. Nerurkar, and A.J. Desai, Organic solvent tolerance of Halobacterium sp. SP1(1) and its extracellular protease, J. Basic Microbiol. 48 (2008), pp. 421-425.
48. R. Usami, T. Fukushima, T. Mizuki, A. Inoue, Y. Yoshida, and K. Horikoshi, Organic solvent tolerance of halophilic archaea, Biosci. Biotechnol. Biochem. 67 (2003), pp. 1809-1812.
49. Y.F. Li, Y. Hata, T. Fujii, T. Hisano, M. Nishihara, T. Kurihara, and N. Esaki, Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism, J. Biol. Chem. 273 (1998), pp. 15035-15044.
50. I.S. Ridder, H.J. Rozeboom, K.H. Kalk, D.B. Janssen, and B.W. Dijkstra, Three-dimensional structure of L-2- haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrate-analogue formate, J. Biol. Chem. 272 (1997), pp. 33015-33022.
51. L. Baldomà and J. Aguilar, Involvement of lactaldehyde dehydrogenase in several metabolic pathways of Escherichia coli K12, J. Biol. Chem. 262 (1987), pp. 13991-13996.
52. D.J. Fairley, D.R. Boyd, N.D. Sharma, C.C. Allen, P. Morgan, and M.J. Larkin, Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift), Appl. Environ. Microbiol. 68 (2002), pp. 6246-6255.
53. J. Feng, Y. Che, J. Milse, Y.J. Yin, L. Liu, C. Rückert, X.H. Shen, S.W. Qi, J. Kalinowski, and S.J. Liu, The gene ncgl2918 encodes a novel maleylpyruvate isomerase that needs mycothiol as cofactor and links mycothiol biosynthesis and gentisate assimilation in Corynebacterium glutamicum, J. Biol. Chem. 281 (2006), pp. 10778-10785.