Genetic tool development underpins recent advances in thermophilic whole-cell biocatalysts

Microbial Biotechnology

Volumn 4, Issue 4, 2011, Pages 438-448

  Taylor, M P ^a,b   van Zyl, L ^a   Tuffin, I M ^a   Leak, D J ^c   Cowan, D A ^a  

^a UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^b TMO Renewables Ltd   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL; CARBOHYDRATE; LIGNOCELLULOSE; PLASMID VECTOR; BIOFUEL; CELLULOSE; ENZYME;

BIOCATALYST; BIOPROCESS; BIOTRANSFORMATION; CELL MEMBRANE PERMEABILITY; ECOLOGICAL NICHE; GENE EXPRESSION; GENE TARGETING; GENE VECTOR; GENETIC ANALYSIS; GENETIC VARIABILITY; HIGH TEMPERATURE; NONHUMAN; PHENOTYPE; PROKARYOTE; SHORT SURVEY; THERMOPHILE; WHOLE CELL; BIOTECHNOLOGY; ENZYMOLOGY; GENETICS; HYDROLYSIS; METABOLIC ENGINEERING; METABOLISM; PROCEDURES; PROKARYOTIC CELL; TEMPERATURE;

PROKARYOTA;

BIOFUELS; BIOTECHNOLOGY; CELLULOSE; ENZYMES; HYDROLYSIS; METABOLIC ENGINEERING; PROKARYOTIC CELLS; TEMPERATURE;

EID: 79960077518     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/j.1751-7915.2010.00246.x     Document Type: Short Survey

References (87)

1. Albers, S.V., and Driessen, A.J. (2008) Conditions for gene disruption by homologous recombination of exogenous DNA into the Sulfolobus solfataricus genome. Archaea 2: 145-149.
2. Angelov, A., and Liebl, W. (2010) Heterologous gene expression in the hyperthermophilic archaeon Sulfolobus solfataricus. Methods Mol Biol 668: 109-116.
3. Atsumi, S., Higashide, W., and Liao, J.C. (2009) Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nat Biotechnol 27: 1177-1180.
4. Beffa, T., Blanc, M., Lyon, P.F., Vogt, G., Marchiani, M., Fischer, J.L., and Aragno, M. (1996) Isolation of Thermus strains from hot composts (60 to 80 degrees C). Appl Environ Microbiol 62: 1723-1727.
5. Berkner, S., and Lipps, G. (2008) Genetic tools for Sulfolobus spp.: vectors and first applications. Arch Microbiol 190: 217-230.
6. Bjornsdottir, S.H., Thorbjarnardottir, S.H., and Eggertsson, G. (2005) Establishment of a gene transfer system for Rhodothermus marinus. Appl Microbiol Biotechnol 66: 675-682.
7. Bjornsdottir, S.H., Blondal, T., Hreggvidsson, G.O., Eggertsson, G., Petursdottir, S., Hjorleifsdottir, S., etal. (2006) Rhodothermus marinus: physiology and molecular biology. Extremophiles 10: 1-16.
8. Bjornsdottir, S.H., Fridjonsson, O.H., Kristjansson, J.K., and Eggertsson, G. (2007) Cloning and expression of heterologous genes in Rhodothermus marinus. Extremophiles 11: 283-293.
9. Borges, N., Matsumi, R., Imanaka, T., Atomi, H., and Santos, H. (2010) Thermococcus kodakarensis mutants deficient in di-myo-inositol phosphate use aspartate to cope with heat stress. J Bacteriol 192: 191-197.
10. Cava, F., Hidalgo, A., and Berenguer, J. (2009) Thermus thermophilus as biological model. Extremophiles 13: 213-231.
11. Childers, S.E., Vargas, M., and Noll, K.M. (1992) Improved methods for cultivation of the extremely thermophilic bacterium Thermotoga neapolitana. Appl Environ Microbiol 58: 3949-3953.
12. Conners, S.B., Mongodin, E.F., Johnson, M.R., Montero, C.I., Nelson, K.E., and Kelly, R.M. (2006) Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species. FEMS Microbiol Rev 30: 872-905.
13. Cripps, R.E., Eley, K., Leak, D.J., Rudd, B., Taylor, M., Todd, M., etal. (2009) Metabolic engineering of Geobacillus thermoglucosidasius for high yield ethanol production. Metab Eng 11: 398-408.
14. Demain, A.L., Newcomb, M., and Wu, J.H. (2005) Cellulase, clostridia, and ethanol. Microbiol Mol Biol Rev 69: 124-154.
15. De Rossi, E., Brigidi, P., Welker, N.E., Riccardi, G., and Matteuzzi, D. (1994) New shuttle vector for cloning in Bacillus stearothermophilus. Res Microbiol 145: 579-583.
16. Desai, S.G., Guerinot, M.L., and Lynd, L.R. (2004) Cloning of l-lactate dehydrogenase and elimination of lactic acid production via gene knockout in Thermoanaerobacterium saccharolyticum JW/SL-YS485 27. Appl Microbiol Biotechnol 65: 600-605.
17. Erauso, G., Marsin, S., Benbouzid-Rollet, N., Baucher, M.F., Barbeyron, T., Zivanovic, Y., etal. (1996) Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: evidence for rolling-circle replication in a hyperthermophile. J Bacteriol 178: 3232-3237.
18. Ernstsson, S., Bjornsdottir, S.H., Jonsson, Z.O., Thorbjarnardottir, S.H., Eggertsson, G., and Palsdottir, A. (2003) Identification and nucleotide sequence analysis of a cryptic plasmid, pRM21, from Rhodothermus marinus. Plasmid 49: 188-191.
19. Friedrich, A., Hartsch, T., and Averhoff, B. (2001) Natural transformation in mesophilic and thermophilic bacteria: identification and characterization of novel, closely related competence genes in Acinetobacter sp. strain BD413 and Thermus thermophilus HB27. Appl Environ Microbiol 67: 3140-3148.
20. Friedrich, A., Prust, C., Hartsch, T., Henne, A., and Averhoff, B. (2002) Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27. Appl Environ Microbiol 68: 745-755.
21. Friedrich, A., Rumszauer, J., Henne, A., and Averhoff, B. (2003) Pilin-like proteins in the extremely thermophilic bacterium Thermus thermophilus HB27: implication in competence for natural transformation and links to type IV pilus biogenesis. Appl Environ Microbiol 69: 3695-3700.
22. Frigaard, N.U., Sakuragi, Y., and Bryant, D.A. (2004a) Gene inactivation in the cyanobacterium Synechococcus sp. PCC 7002 and the green sulfur bacterium Chlorobium tepidum using in vitro-made DNA constructs and natural transformation. Methods Mol Biol 274: 325-340.
23. Frigaard, N.U., Maresca, J.A., Yunker, C.E., Jones, A.D., and Bryant, D.A. (2004b) Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum. J Bacteriol 186: 5210-5220.
24. Fukui, T., Atomi, H., Kanai, T., Matsumi, R., Fujiwara, S., and Imanaka, T. (2005) Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res 15: 352-363.
25. Georgieva, T.I., Mikkelsen, M.J., and Ahring, B.K. (2007) High ethanol tolerance of the thermophilic anaerobic ethanol producer Thermoanaerobacter BG1L1. Cent Eur J Biol 2: 364-377.
26. Gerday, G., and Glansdorff, N. (2007) Physiology and Biochemistry of Extremophiles. Washington, DC, USA: American Society for Microbiology.
27. de Grado, M., Castan, P., and Berenguer, J. (1999) A high-transformation-efficiency cloning vector for Thermus thermophilus. Plasmid 42: 241-245.
28. Haki, G.D., and Rakshit, S.K. (2003) Developments in industrially important thermostable enzymes: a review. Bioresour Technol 89: 17-34.
29. Hartley, B.S., and Sharma, G. (1987) Novel ethanol fermentations from sugar cane and straw. Philos Trans R Soc Lond A 321: 555-568.
30. Iwai, M., Katoh, H., Katayama, M., and Ikeuchi, M. (2004) Improved genetic transformation of the thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1. Plant Cell Physiol 45: 171-175.
31. Jenney, F.E., Jr, and Adams, M.W. (2008) Hydrogenases of the model hyperthermophiles. Ann N Y Acad Sci 1125: 252-266.
32. Kanai, T., Imanaka, H., Nakajima, A., Uwamori, K., Omori, Y., Fukui, T., etal. (2005) Continuous hydrogen production by the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1. J Biotechnol 116: 271-282.
33. Klapatch, T.R., Guerinot, M.L., and Lynd, L.R. (1996) Electrotransformation of Clostridium thermosaccharolyticum. J Ind Microbiol 16: 342-347.
34. Koyama, Y., Hoshino, T., Tomizuka, N., and Furukawa, K. (1986) Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp. J Bacteriol 166: 338-340.
35. Koyama, Y., Arikawa, Y., and Furukawa, K. (1990) A plasmid vector for an extreme thermophile, Thermus thermophilus. FEMS Microbiol Lett 60: 97-101.
36. Leveque, E., Haye, B., and Belarbi, A. (2000) Cloning and expression of an alpha-amylase encoding gene from the hyperthermophilic archaebacterium Thermococcus hydrothermalis and biochemical characterisation of the recombinant enzyme. FEMS Microbiol Lett 186: 67-71.
37. Lucas, S., Toffin, L., Zivanovic, Y., Charlier, D., Moussard, H., Forterre, P., etal. (2002) Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi. Appl Environ Microbiol 68: 5528-5536.
38. Lyon, P.F., Beffa, T., Blanc, M., Auling, G., and Aragno, M. (2000) Isolation and characterization of highly thermophilic xylanolytic Thermus thermophilus strains from hot composts. Can J Microbiol 46: 1029-1035.
39. Mai, V., and Wiegel, J. (2000) Advances in development of a genetic system for Thermoanaerobacterium spp.: expression of genes encoding hydrolytic enzymes, development of a second shuttle vector, and integration of genes into the chromosome. Appl Environ Microbiol 66: 4817-4821.
40. Mai, V., Lorenz, W.W., and Wiegel, J. (1997) Transformation of Thermoanaerobacterium sp. strain JW/SL-YS485 with plasmid pIKM1 conferring kanamycin resistance. FEMS Microbiology Lett 148: 163-167.
41. Martins, L.O., Empadinhas, N., Marugg, J.D., Miguel, C., Ferreira, C., Costa, M.S., and Santos, H. (1999) Biosynthesis of mannosylglycerate in the thermophilic bacterium Rhodothermus marinus. Biochemical and genetic characterization of a mannosylglycerate synthase. J Biol Chem 274: 35407-35414.
42. Matsumura, M., and Aiba, S. (1985) Screening for thermostable mutant of kanamycin nucleotidyltransferase by the use of a transformation system for a thermophile, Bacillus stearothermophilus. J Biol Chem 260: 15298-15303.
43. Matsumi, R., Manabe, K., Fukui, T., Atomi, H., and Imanaka, T. (2007) Disruption of a sugar transporter gene cluster in a hyperthermophilic archaeon using a host-marker system based on antibiotic resistance. J Bacteriol 189: 2683-2691.
44. Maurelli, L., Giovane, A., Esposito, A., Moracci, M., Fiume, I., Rossi, M., and Morana, A. (2008) Evidence that the xylanase activity from Sulfolobus solfataricus Oalpha is encoded by the endoglucanase precursor gene (sso1354) and characterization of the associated cellulase activity. Extremophiles 12: 689-700.
45. Mohr, G., Ghanem, E., and Lambowitz, A.M. (2010) Mechanisms used for genomic proliferation by thermophilic group II introns. PLoS Biol 8: e1000391.
46. Moreno, R., Zafra, O., Cava, F., and Berenguer, J. (2003) Development of a gene expression vector for Thermus thermophilus based on the promoter of the respiratory nitrate reductase. Plasmid 49: 2-8.
47. Muhlenhoff, U., and Chauvat, F. (1996) Gene transfer and manipulation in the thermophilic cyanobacterium Synechococcus elongatus. Mol Gen Genet 252: 93-100.
48. Natarajan, M.R., and Oriel, P. (1991) Conjugal transfer of recombinant transposon Tn916 from Escherichia coli to Bacillus stearothermophilus. Plasmid 26: 67-73.
49. Niehaus, F., Peters, A., Groudieva, T., and Antranikian, G. (2000) Cloning, expression and biochemical characterisation of a unique thermostable pullulan-hydrolysing enzyme from the hyperthermophilic archaeon Thermococcus aggregans. FEMS Microbiol Lett 190: 223-229.
50. Noll, K.M., and Vargas, M. (1997) Recent advances in genetic analyses of hyperthermophilic archaea and bacteria. Arch Microbiol 168: 73-80.
51. Pantazaki, A.A., Pritsa, A.A., and Kyriakidis, D.A. (2002) Biotechnologically relevant enzymes from Thermus thermophilus. Appl Microbiol Biotechnol 58: 1-12.
52. Park, H.S., Kayser, K.J., Kwak, J.H., and Kilbane, J.J., 2nd (2004) Heterologous gene expression in Thermus thermophilus: beta-galactosidase, dibenzothiophene monooxygenase, PNB carboxy esterase, 2-aminobiphenyl-2, 3-diol dioxygenase, and chloramphenicol acetyl transferase. J Ind Microbiol Biotechnol 31: 189-197.
53. Peng, H., Fu, B.L., Mao, Z.G., and Shao, W.L. (2006) Electrotransformation of Thermoanaerobacter ethanolicus JW200. Biotechnol Lett 28: 1913-1917.
54. Peteranderl, R., Shotts, E.B., Jr, and Wiegel, J. (1990) Stability of antibiotics under growth conditions for thermophilic anaerobes. Appl Environ Microbiol 56: 1981-1983.
55. Robb, F., Antranikian, G., Grogan, D., and Driessen, A. (2008) Thermophiles: Biology and Technology at High Temperatures. Robb, F., Antranikian, G., Grogan, D., and Driessen, A. (eds). Boca Raton, FL, USA: CRC Press.
56. Roberts, M.F. (2005) Organic compatible solutes of halotolerant and halophilic microorganisms. Saline Systems 1: 5.
57. Rumszauer, J., Schwarzenlander, C., and Averhoff, B. (2006) Identification, subcellular localization and functional interactions of PilMNOWQ and PilA4 involved in transformation competency and pilus biogenesis in the thermophilic bacterium Thermus thermophilus HB27. FEBS J 273: 3261-3272.
58. Sander, J., Nowaczyk, M., Buchta, J., Dau, H., Vass, I., Deak, Z., etal. (2010) Functional characterization and quantification of the alternative PsbA copies in Thermosynechococcus elongatus and their role in photoprotection. J Biol Chem 285: 29851-29856.
59. Santangelo, T.J., and Reeve, J.N. (2010) Deletion of switch 3 results in an archaeal RNA polymerase that is defective in transcript elongation. J Biol Chem 285: 23908-23915.
60. Santangelo, T.J., Cubonova, L., and Reeve, J.N. (2008) Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl Environ Microbiol 74: 3099-3104.
61. Sato, T., Fukui, T., Atomi, H., and Imanaka, T. (2003) Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol 185: 210-220.
62. Sato, T., Fukui, T., Atomi, H., and Imanaka, T. (2005) Improved and versatile transformation system allowing multiple genetic manipulations of the hyperthermophilic archaeon Thermococcus kodakaraensis. Appl Environ Microbiol 71: 3889-3899.
63. Sen, S., and Oriel, P. (1990) Transfer of transposon Tn916 from Bacillus subtilis to Thermus aquaticus. FEMS Microbiol Lett 55: 131-134.
64. Shaw, A.J., Podkaminer, K.K., Desai, S.G., Bardsley, J.S., Rogers, S.R., Thorne, P.G., etal. (2008) Metabolic engineering of a thermophilic bacterium to produce ethanol at high yield. Proc Natl Acad Sci USA 105: 13769-13774.
65. Shaw, A.J., Hogsett, D.A., and Lynd, L.R. (2010) Natural competence in Thermoanaerobacter and Thermoanaerobacterium species. Appl Environ Microbiol 76: 4713-4719.
66. She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M.J., etal. (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci USA 98: 7835-7840.
67. She, Q., Zhang, C., Deng, L., Peng, N., Chen, Z., and Liang, Y.X. (2009) Genetic analyses in the hyperthermophilic archaeon Sulfolobus islandicus. Biochem Soc Trans 37: 92-96.
68. Shestakov, S.V., and Khyen, N.T. (1970) Evidence for genetic transformation in blue-green alga Anacystis nidulans. Mol Gen Genet 107: 372-375.
69. Sommer, P., Georgieva, T., and Ahring, B.K. (2004) Potential for using thermophilic anaerobic bacteria for bioethanol production from hemicellulose. Biochem Soc Trans 32: 283-289.
70. Studholme, D.J., Jackson, R.A., and Leak, D.J. (1999) Phylogenetic analysis of transformable strains of thermophilic Bacillus species. FEMS Microbiol Lett 172: 85-90.
71. Tamakoshi, M., Uchida, M., Tanabe, K., Fukuyama, S., Yamagishi, A., and Oshima, T. (1997) A new Thermus-Escherichia coli shuttle integration vector system. J Bacteriol 179: 4811-4814.
72. Tamakoshi, M., Yaoi, T., Oshima, T., and Yamagishi, A. (1999) An efficient gene replacement and deletion system for an extreme thermophile, Thermus thermophilus. FEMS Microbiol Lett 173: 431-437.
73. Taylor, M.P., Esteban, C.D., and Leak, D.J. (2008) Development of a versatile shuttle vector for gene expression in Geobacillus spp. Plasmid 60: 45-52.
74. Taylor, M.P., Eley, K.L., Martin, S., Tuffin, M.I., Burton, S.G., and Cowan, D.A. (2009) Thermophilic ethanologenesis: future prospects for second-generation bioethanol production. Trends Biotechnol 27: 398-405.
75. Turner, P., Mamo, G., and Karlsson, E.N. (2007) Potential and utilization of thermophiles and thermostable enzymes in biorefining. Microb Cell Fact 6: 9.
76. Tyurin, M.V., Desai, S.G., and Lynd, L.R. (2004) Electrotransformation of Clostridium thermocellum. Appl Environ Microbiol 70: 883-890.
77. Tyurin, M.V., Lynd, L.R., and Wiegel, J. (2006) Gene transfer systems for obligately anaerobic thermophilic bacteria. Extremophiles 35: 309-330.
78. Waege, I., Schmid, G., Thumann, S., Thomm, M., and Hausner, W. (2010) Shuttle vector-based transformation system for Pyrococcus furiosus. Appl Environ Microbiol 76: 3308-3313.
79. Wahlund, T.M., and Madigan, M.T. (1995) Genetic transfer by conjugation in the thermophilic green sulfur bacterium Chlorobium tepidum. J Bacteriol 177: 2583-2588.
80. Wang, F., Zhang, S., Huang, Q., Shen, Y., and Ni, J. (2009) Advances in genetic manipulation systems of hyperthermophilic archaea-a review. Wei Sheng Wu Xue Bao 49: 1418-1423.
81. Wayne, J., and Xu, S.Y. (1997) Identification of a thermophilic plasmid origin and its cloning within a new Thermus-E. coli shuttle vector. Gene 195: 321-328.
82. Weber, J.M., Johnson, S.P., Vonstein, V., Casadaban, M.J., and Demirjian, D.C. (1995) A chromosome integration system for stable gene transfer into Thermus flavus. Biotechnology (N Y) 13: 271-275.
83. van de Werken, H.J., Verhaart, M.R., VanFossen, A.L., Willquist, K., Lewis, D.L., Nichols, J.D., etal. (2008) Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Appl Environ Microbiol 74: 6720-6729.
84. Wu, L.J., and Welker, N.E. (1989) Protoplast transformation of Bacillus stearothermophilus NUB36 by plasmid DNA. J Gen Microbiol 135: 1315-1324.
85. Yao, S., and Mikkelsen, M.J. (2010) Metabolic engineering to improve ethanol production in Thermoanaerobacter mathranii. Appl Microbiol Biotechnol 88: 199-208.
86. Yu, J.S., Vargas, M., Mityas, C., and Noll, K.M. (2001) Liposome-mediated DNA uptake and transient expression in Thermotoga. Extremophiles 5: 53-60.
87. Zeikus, J.G., Ben-Bassat, A., Ng, T.K., and Lamed, R.J. (1981) Thermophilic ethanol fermentations. Basic Life Sci 18: 441-461.