Differentiation of a Hyperthermophilic Archaeon Pyrococcus sp. strain Pikanate 5017, by Arbitrarily Primed PCR
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Keywords:
Thermococcales Pyrococcus Thermococcus fingerprint hyperthermophile hot spring
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Abstract
Pyrococcus and Thermococcus are hyperthermophilic archaea in the order Thermococcales. Bothgenera are strictly anaerobes, gaining energy by fermentation of peptide and several carbohydrates at optimaltemperature above 70 °C. A Pyrococcus sp. strain Pikanate 5017 (PK 5017) was recently isolated from ahot spring in Northern Thailand. The strain PK 5017 is a valuable source of numerous genes encodingthermostable enzymes. Growth kinetics determined at various temperatures (75-105 °C) indicates that strainPK5017 is a fast growing archaeon. An arbitrarily primed PCR (AP-PCR) technique was successfully appliedto differentiate the genome sequences of six members of Thermococcales. Two single primers, ARB-1f(5’ ATGAG GACT GAAA CCATT 3’) and ARB-2f (5’ GTAAA ACGA CGGC CAGT 3’), are effectivein producing polymorphisms of the PCR products at 3-10 ng of DNAs. The unique AP-PCR fingerprintsdistinguish the strain PK5017 from P. furiosus, P. horikoshii, P. abyssi, T. litoralis, and T. celer. The resultsindicate a clear distinction of genome sequences among Pyrococcus and Thermococcus genera.
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Pasomsup, P., González, J. M., Portillo, M. C., Pongsapukdee, V., & Kanoksilapatham, W. (2013). Differentiation of a Hyperthermophilic Archaeon Pyrococcus sp. strain Pikanate 5017, by Arbitrarily Primed PCR. Science, Engineering and Health Studies, 5(1), 14–23. https://doi.org/10.14456/sustj.2011.10
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Research Articles
References
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Stetter, K. O., Huber, R., Blochl, E., Kurr, M., Eden, R. D., Fielder, M., Cash, H. and Vance, I. (1993). Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature, 365: 743-745.
Stetter, K. O. (1996). Hyperthermophilic prokaryotes. FEMS Microbiology Reviews, 18: 149-158.
Takai, K., Sugal, A., Itoh, T. H. and Horikoshi, K. (2000). Palaeococcus ferrophilus gen. nov.,sp.nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. International Journal of Systematic and Evolutionary Microbiology, 50: 489-500, 2000.
Welsh, J. and McClelland, M. (1990). Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research, 19: 7213-7218.
Welsh, J. and McClelland, M. (1991). Genomic fringerprints produced by PCR with consensus tRNA gene primers. Nucleic Acids Research, 19: 861-866.
Welsh, J., Petersen, C., and McClelland, M. (1991). Polymorphisms generated by arbitrarily primed PCR in the mouse: application to strain identification and genetic mapping. Nucleic Acids Research, 19: 303-306.
Woese, C. R., Kandler, O., and Wheelis, M. L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences USA, 87: 4576-4579.
Zillig, W., Holz, I., Janekovic, D., Scha ̈fer, W., and Reiter, W. D. (1983). The Archebacterium Thermococcus celer represents, a novel genus within the thermophilic branch of the archaebacteria. Systematic and Applied Microbiology, 4: 88-94.
Zillig, W., Holz, I., Klenk, H-P., Trent. J., Wunderl, S., Janekovic, D., Imsel, E., and Haas, B. (1987). Pyrococcus woesei sp. nov., an ultra-Thermophilic marine archaebacterium, representing a novel order, Thermococcales. Systematic and Applied Microbiology, 9: 62-70.
Barbier, G., Godfroy, A., Meunier, J. R., Quérellou, J., Cambon, M. A., Lesongeur, F., Grimont, P. A., and Raguénès, G. (1999). Pyrococcus glycovorans sp. nov., a hyperthermophilic archaeon isolated from the East Pacific Rise. International Journal of Systematic Bacteriology, 49(Pt 4): 1829-1937.
Charbonnier, F. and Forterre, P. (1995). Purification of plasmids from thermophilic and hyperthermophilic archaea. In Archaea, a Laboratory Manual, Thermophiles. (Robb, F. T. and Place A. R., eds.) pp. 87-90. Cold Spring Harbor Laboratory, New York: Cold Spring Harbor.
Erauso, G., Reysenbach, A. L., Godfroy, A., Meunier, J. R., Crump, B., Partensky, F., Baross, J. A., Marteinsson, V., Barbier, G., Pace, N.R., and Prieur, D. (1993). Pyrococcus abyssi, sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Archieves of Microbiology, 160: 338-349.
Fiala, G. and Stetter K. O. (1986). Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C. Archieves of Microbiology, 145: 56-61.
González, J. M., Masuchi, Y., Robb, F. T., Ammerman, W., Maeder, D. L., Yanagibayashi, M., Tamaoka, J., and Kato, C. (1998) Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough. Extremophiles, 2: 123-130.
González, J. M., Sheckells, D., Vareike, M., Kupratkina, D., Borges, K., and Robb, F. T. (1999). Thermococcus waiotapuensis sp. nov., a hyperthermophilic archaeon from freshwater hot springs in New Zealand. Archieves of Microbiology, 172: 95-101.
Huber, R., Stöhr, J., Honenhaus, S., Rachel, R., Burggraf, S., Jannash, H. W., and Stetter, K. O. (1995). Thermococcus chitonophagus sp. nov., a novel, chitin-degrading, hyperthermophilic archaeum from a deep-sea hydrothermal vent. Archieves of Microbiology, 164: 255-264.
Kanoksilapatham, W., González, J. M., Maeder, D. L., DiRuggiero, J., and Robb, F. T. (2004). A proposal to rename the hyperthermophile Pyrococcus woesei as Pyrococcus furiosus, sub sp. woesei. Archaea, 1: 277-283.
Kecha, M., Benallaoua, S., Touzel, J. P., Bonaly, R. and Duchiron F. (2007). Biochemical and phylogenetic characterization of a novel terrestrial hyperthermophilic archaeon pertaining to the genus Pyrococcus from
an Algerian hydrothermal hot spring. Extremophiles, 11: 65-73.
Keller, M., Braun, F-J., Dirmeier, R., Hafenbradl, D., Burggraf, S., Rachel, R., and Stetter, K. O. (1995). Thermococcus alcaliphilus sp. nov., a new hyperthermophilic archaeum growing on polysulfide at alkaline pH. Archieves of Microbiology, 164: 390-395.
Kobayashi, T., Kwak, Y. S., Akiba, T., Kudo, T., and Horikoshi, K. (1994). Thermococcus profundus sp. nov., a new hyperthermophilic archaeum isolated from a deep-sea hydrohermal vent. Systematic and Applied Microbiology, 17: 232-236.
Miroshnichenko, M. L., Hippe, H., Stackebrandt, E., Kostrikina, N. A., Chernyh, N. A., Jeanthon, C., Nazina, T. N., Belyyaev, S. S., and Bonch-Osmolovskaya, E. A. (2001). Isolation and characterization of Thermococcus sibiricus sp. nov. from a Western Siberia high-temperature oil reservoir. Extremophiles, 5: 85-91.
Neuner, A., Jannasch, H. W., Belkin, S., and Stetter, K. O. (1990). Thermococcus litoralis sp. nov.: a new species of extremely thermophilic marine archaebacteria. Archieves of Microbiology, 153: 205-207.
Pikuta, E. V., Marsic, D., Itoh, T., Bej, A. K., Tang, J., Whitman, W. B., Ng J. D., Garriott, O. K., and Hoover, R. B. (2007). Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology, 57(Pt 7): 1612-1618.
Ronimus, R. S., Reysenbach, A L., Musgrave, D. R., and Morgan, H. W. (1997). The phylogenetic position of the Thermococcus isolate AN1 based on 16S rRNA gene sequence analysis: a proposal that AN1 represents a new species, Thermococcus zilligii sp. nov. Archieves of Microbiology, 168: 245-248.
Stetter, K. O., Huber, R., Blochl, E., Kurr, M., Eden, R. D., Fielder, M., Cash, H. and Vance, I. (1993). Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature, 365: 743-745.
Stetter, K. O. (1996). Hyperthermophilic prokaryotes. FEMS Microbiology Reviews, 18: 149-158.
Takai, K., Sugal, A., Itoh, T. H. and Horikoshi, K. (2000). Palaeococcus ferrophilus gen. nov.,sp.nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. International Journal of Systematic and Evolutionary Microbiology, 50: 489-500, 2000.
Welsh, J. and McClelland, M. (1990). Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research, 19: 7213-7218.
Welsh, J. and McClelland, M. (1991). Genomic fringerprints produced by PCR with consensus tRNA gene primers. Nucleic Acids Research, 19: 861-866.
Welsh, J., Petersen, C., and McClelland, M. (1991). Polymorphisms generated by arbitrarily primed PCR in the mouse: application to strain identification and genetic mapping. Nucleic Acids Research, 19: 303-306.
Woese, C. R., Kandler, O., and Wheelis, M. L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences USA, 87: 4576-4579.
Zillig, W., Holz, I., Janekovic, D., Scha ̈fer, W., and Reiter, W. D. (1983). The Archebacterium Thermococcus celer represents, a novel genus within the thermophilic branch of the archaebacteria. Systematic and Applied Microbiology, 4: 88-94.
Zillig, W., Holz, I., Klenk, H-P., Trent. J., Wunderl, S., Janekovic, D., Imsel, E., and Haas, B. (1987). Pyrococcus woesei sp. nov., an ultra-Thermophilic marine archaebacterium, representing a novel order, Thermococcales. Systematic and Applied Microbiology, 9: 62-70.