1887

Chapter 4 : Enzymes from Extreme Environments

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $30.00

Preview this chapter:
Zoom in
Zoomout

Enzymes from Extreme Environments, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816827/9781555815127_Chap04-1.gif /docserver/preview/fulltext/10.1128/9781555816827/9781555815127_Chap04-2.gif

Abstract:

This chapter presents a number of methods that have been successfully applied in the screening for enzymes from extremophilic microorganisms and their communities. Parameters such as temperature, pH, percentage of relative humidity, salinity, dO, redox state, moisture content, light, local geology, weather (cloud, precipitation, wind speed), and so on, may be critical or irrelevant. Thermophilic samples, psychrophilic samples, halophilic samples, acidophilic samples, superficial sea- and freshwater samples are the issues for consideration in the sampling of various specific extreme environments. Two major extraction protocols may be used: (i) phenol extraction, where the gentle hydrophobicity of phenol makes it a good solvent for DNA extraction, and (ii) the use of commercial kits. Extremophiles are an obvious source of novel enzymes that may revolutionize the biofuels industry. Several bacterial and fungal species produce ligninases, with the enzymes produced by brown- and white-rot fungi being studied the most extensively. A report by Tuncer and his coworkers found that the ratio of carbon (C)/nitrogen (N) affected enzyme production and that a C/N ratio of 4:1 to 5.3:1 resulted in maximal enzyme production. This report also highlighted the need to grow all test strains on a range of different carbon sources, because the amount of extracellular enzymes produced varies depending on the carbon source, and it is essential to find the best medium for enzyme production. There is certainly a need for standardized methods for performing metagenomics projects, from physical-chemical description of sampling sites and sampling procedures down to the data interpretation and integration.

Citation: Cowan D, Kirby B, Meiring T, Ferrer M, Guazzaroni M, Golyshina O, Golyshin P. 2010. Enzymes from Extreme Environments, p 43-61. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch4

Key Concept Ranking

Bacteria and Archaea
0.48143873
Microbial Ecology
0.48143873
Bacterial Cell Wall
0.4456354
Denaturing Gradient Gel Electrophoresis
0.4211915
0.48143873
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Vector map of the shuttle fosmid pCT3FK (Chl, chloramphenicol resistance; kat, thermostable kanamycin resistance) and the region of HB27 genome containing the genes. G3PDH, glycerol-3-phosphate dehy-drogenase; hyp, hypothetical protein ( ).

Citation: Cowan D, Kirby B, Meiring T, Ferrer M, Guazzaroni M, Golyshina O, Golyshin P. 2010. Enzymes from Extreme Environments, p 43-61. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555816827.ch04
1. Adhi, T. D.,, R. A. Korus, and, D. L. Crawford. 1989. Production of major extracellular enzymes during lignocel-lulose degradation by two streptomycetes in agitated submerged culture. Appl. Environ. Microbiol. 55:11651168.
2. Andexer, J.,, J. K. Guterl,, M. Pohl, and, T. Eggert. 2006. A high-throughput screening assay for hydroxynitrile lyase activity. Chem. Commun. (Camb.) 40:42014203.
3. Angelov, A.,, M. Mientus,, S. Liebl, and, W. Liebl. 2009. A two-host fosmid system for functional screening of (meta) genomic libraries from extreme thermophiles. Syst. Appl. Microbiol. 32:177185.
4. Aparicio, T.,, P. Lorenzo, and, J. Perera. 2000. pT3.2I, the smallest plasmid of Thiobacillus T3.2. Plasmid 44:111.
5. Bachmann, S. L., and, A. J. McCarthy. 1989. Purification and characterisation of a thermostable (β-xylosidase from Thermomonospora fusca. J. Gen. Microbiol. 135:293299.
6. Baminger, U.,, B. Nidetzky,, K. D. Kulbe, and, D. Haltrich. 1999. A simple assay for measuring cellobiose dehydrogenase in the presence of laccase. J. Microbiol. Methods 35:253259.
7. Bauer, M.,, L. Marschaus,, M. Reuff,, V. Besche,, S. Sartorius-Neef, and, F. Pfeifer. 2008. Overlapping activator sequences determined for two oppositely oriented promoters in halophilic Archaea. Nucleic Acids Res. 36:598606.
8. Beloqui, A.,, P. D. de María,, P. N. Golyshin, and, M. Ferrer. 2008. Recent trends in industrial microbiology. Curr. Opin. Microbiol. 11:204248.
9. Berkner, S.,, D. Grogan,, S. V. Albers, and, G. Lipps. 2007. Small multicopy, non-integrative shuttle vectors based on the plasmid pRN1 for Sulfolobus acidocaldarius and Sulfolobus solfataricus, model organisms of the (cren-) archaea. Nucleic Acids Res. 35:e88.
10. Berkner, S., and, G. Lipps. 2008. Genetic tools for Sulfolobus spp.: vectors and first applications. Arch. Microbiol. 190:217230.
11. Bernfeld, P. 1955. Amylases alpha and beta. Methods Enzymol. 1:149158.
12. Biddle, J. F.,, S. Fitz-Gibbon,, S. C. Schuster,, J. E. Brenchley, and, C.H. House. 2008. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc. Natl. Acad. Sci. USA 105:1058310588.
13. Bjerre, A. B.,, A. Bjerring Olesen,, T. Fernqvist,, A. Ploger, and, A. Skammelsen Schmidt. 1996. Pretreatment of wheat straw using combined wet oxidation and alkaline hydrolysis resulting in convertible cellulose and hemicel-lulose. Biotechnol. Bioeng. 49:568577.
14. Cava, F.,, A. Hidalgo, and, J. Berenguer. 2009. Ther-mus thermophilus as biological model. Extremophiles 13:213231.
15. Chautard, H.,, E. Blas-Galindo,, T. Menguy,, L. Grand’Moursel,, F. Cava,, J. Berenguer, and, M. Delcourt. 2007. An activity-independent selection system of thermostable protein variants. Nat. Methods 4:919921.
16. Chen, L.,, K. Brugger,, M. Skovgaard,, P. Redder,, Q. She,, E. Torarinsson,, B. Greve,, M. Awayez,, A. Zibat,, H. P. Klenk, and, R. A. Garrett. 2005. The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J. Bacteriol. 187:49924999.
17. Cohen, G. N.,, V. Barbe,, D. Flament,, M. Galperin,, R. Heilig,, O. Lecompte,, O. Poch,, D. Prieur,, J. Querellou,, R. Ripp,, J. C. Thierry,, J. Van der Oost,, J. Weissenbach,, Y. Zivanovic, and, P. Forterre. 2003. An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol. Microbiol. 47:14951512.
18. Courtois, S.,, C. M. Cappellano,, M. Ball,, F. X. Francou,, P. Normand,, G. Helynck,, A. Martinez,, S. J. Kolvek,, J. Hopke,, M. S. Osburne,, P. R. August,, R. Nalin,, M. Guerineau,, P. Jeannin,, P. Simonet, and, J. L. Pernodet. 2003. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl. Environ. Microbiol. 69:4955.
19. Cowan, D. 1992. Enzymes from thermophilic archaebacteria: current and future applications in biotechnology, p. 149169. In M. J. Danson,, D. W. Hough, and, G. G. Lunt (ed.), The Archaebacteria: Biochemistry and Biotechnology. Portland Press, London, United Kingdom.
20. Daniel, R. M.,, M. J. Danson,, D. W. Hough,, C. K. Lee,, M. E. Peterson, and, D. A. Cowan. 2008. Enzyme stability and activity at high temperatures, p. 134. In K. S. Sid-diqui and, T. Thomas (ed.), Protein Adaptation in Extremo-philes. Nova Science Publishers Inc., New York, NY.
21. Dawson, R. M. C.,, D. C. Elliot,, W. H. Elliot, and, K. M. Jones. 1986. Data for Biochemical Research, 3rd ed. Oxford Science Publications, Oxford, United Kingdom.
22. De Castro, R. E.,, D. M. Ruiz,, M. I. Gimenez,, M. X. Silveyra,, R. A. Paggi, and, J. A. Maupin-Furlow. 2008. Gene cloning and heterologous synthesis of a haloalka-liphilic extracellular protease of Natrialba magadii (Nep). Extremophiles 12:677687.
23. de Grado, M.,, P. Castán, and, J. Berenguer. 1999. A high-transformation efficiency cloning vector for Thermus thermophilus. Plasmid 42:241245.
24. de Grado, M.,, I. Lasa, and, J. Berenguer. 1998. Characterization of a plasmid replicative origin from an extreme thermophile. FEMS Microbiol. Lett. 165:5157.
25. de Groot, N. S., and, S. Ventura. 2006. Effect of temperature on protein quality in bacterial inclusion bodies. FEBS Lett. 580:64716476.
26. DeLong, E.F. 2009. The microbial ocean from genomes to biomes. Nature 459:200206.
27. Dock, C.,, M. Hess, and, G. Antranikian. 2008. A ther-moactive glucoamylase with biotechnological relevance from the thermoacidophilic Euryarchaeon Thermoplasma acidophilum. Appl. Microbiol. Biotechnol. 78:105114.
28. Dos Santos, V. A.,, S. Heim,, E. R. Moore,, M. Stratz, and, K. N. Timmis. 2004. Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ. Microbiol. 6:12641286.
29. Dyall-Smith, M. 2008. The Halohandbook: Protocols for Haloarchaeal Genetics. http://www.haloarchaea.com. [Online.] Accessed 30 April 2009.
30. Feller, G. 2008. Enzyme function at low temperatures in psychrophiles, p. 3570. In K. S. Siddiqui and, T. Thomas (ed.), Protein Adaptation in Extremophiles. Nova Science Publishers Inc., New York, NY.
31. Feller, G., and, C. Gerday. 2003. Psychrophilic enzymes: hot topics in cold adaptation. Nat. Rev. Microbiol. 1:200208.
32. Ferrer, M.,, A. Beloqui,, K. N. Timmis, and, P. N. Golyshin. 2008. Metagenomics for mining new genetic resources of microbial communities. J. Mol. Microbiol. Biotechnol. 16:109123.
33. Ferrer, M.,, A. Beloqui,, J. M. Vieites,, M. E. Guazzaroni,, I. Berger, and, A. Aharoni. 2009. Interplay of metagenom-ics and in vitro compartmentalization. Microbial Biotechnol. 2:3139.
34. Fish, S. A.,, A. W. Duckworth, and, W. D. Grant. 1999. Novel plasmids from alkaliphilic halomonads. Plasmid 41:268273.
35. Gabor, E. M.,, E. J. de Vries, and, D. B. Janssen. 2004. Construction, characterization, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases. Environ. Microbiol. 6:948958.
36. Geddie, M. L.,, L. A. Rowe,, O. B. Alexander, and, I. Matsumura. 2004. High throughput microplate screens for directed protein evolution. Methods Enzymol. 388:134145.
37. Gilead, S., and, Y. Shoham. 1995. Purification and characterization of a-l-arabinofuranosidase from Bacillus stea-rothermophilus T-6. Appl. Environ. Microbiol. 61:170174.
38. Giver, L.,, A. Gershenson,, P. O. Freskgard, and, F. H. Arnold. 1998. Directed evolution of a thermostable esterase. Proc. Natl. Acad. Sci. USA 95:1280912813.
39. Grant, W. D.,, R. T. Gemmell, and, T. J. McGenity. 1998. Halophiles, p. 93132. In K. Horikoshi and, W. D. Grant (ed.), Extremophiles—Microbial Life in Extreme Environments. Wiley-Liss Inc., New York, NY.
40. Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669685.
41. Handelsman, J. 2008. Metagenomics is not enough. DNA Cell Biol. 27:219221.
42. Henne, A.,, H. Bruggemann,, C. Raasch,, A. Wiezer,, T. Hartsch,, H. Liesegang,, A. Johann,, T. Lienard,, O. Gohl,, R. Martinez-Arias,, C. Jacobi,, V. Starkuviene,, S. Schlenczeck,, S. Dencker,, R. Huber,, H. P. Klenk,, W. Kramer,, R. Merkl,, G. Gottschalk, and, H. J. Fritz. 2004. The genome sequence of the extreme thermophile Thermus thermophilus. Nat. Biotechnol. 22:547553.
43. Henriksson, G.,, G. Johansson, and, G. Pettersson. 2000. A critical review of cellobiose dehydrogenases. J. Biotechnol. 78:93113.
44. Hering, O.,, M. Brenneis,, J. Beer,, B. Suess, and, J. Soppa. 2009. A novel mechanism for translation initiation operates in haloarchaea. Mol. Microbiol. 71:14511463.
45. Hess, M. 2008. Thermoacidophilic proteins for biofuel production. Trends Microbiol. 16:414419.
46. Hidalgo, A.,, L. Betancor,, R. Moreno,, O. Zafra,, F. Cava,, R. Fernandez-Lafuente,, J. M. Guisan, and, J. Berenguer. 2004. Thermus thermophilus as a cell factory for the production of a thermophilic Mn-dependent catalase which fails to be synthesized in an active form in Escherichia coli. Appl. Environ. Microbiol. 70:38393844.
47. Hiromi, K.,, Y. Takahashi, and, S. Ono. 1963. Kinetics of hydrolytic reaction catalyzed by crystalline bacterial ot-amylase. The influence of temperature. Bull. Chem. Soc. Jpn. 36:563569.
48. Holmes, M. L.,, S. D. Nuttall, and, M. L. Dyall-Smith. 1991. Construction and use of halobacterial shuttle vectors and further studies on Haloferax DNA gyrase. J. Bacteriol. 173:38073813.
49. Holmes, M.,, R Pfeifer, and, M. Dyall-Smith. 1994. Improved shuttle vectors for Haloferax volcanii including a dual-resistance plasmid. Gene 146:117121.
50. Horikoshi, K. 1971. Production of alkaline enzymes by alkalophilic microorganisms. II. Alkaline amylase production by Bacillus No. A-40–2. Agric. Biol. Chem. 35:17831791.
51. Horikoshi, K. 1998. Alkaliphiles, p. 155180. In K. Horikoshi and, W. D. Grant (ed.), Extremophiles—Microbial Life in Extreme Environments. Wiley-Liss Inc., New York, NY.
52. Hunke, S., and, J. M. Betton. 2003. Temperature effect on inclusion body formation and stress response in the peri-plasm of Escherichia coli. Mol. Microbiol. 50:15791589.
53. Ingham, C. J.,, A. Sprenkels,, J. Bomer,, D. Molenaar,, A. van den Berg,, J. E. van Hylckama Vlieg, and, W. M. de Vos. 2007. The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc. Natl. Acad. Sci. USA 104:1821718222.
54. Jenney, F E., Jr., and, M. W. Adams. 2008. The impact of extremophiles on structural genomics (and vice versa). Extremophiles 12:3950.
55. Jolley, K. A.,, E. Rapaport,, D. W. Hough,, M. J. Danson,, W. G. Woods, and, M. L. Dyall-Smith. 1996. Dihydro-lipoamide dehydrogenase from the halophilic archaeon Haloferax volcanii: homologous overexpression of the cloned gene. J. Bacteriol. 178:30443048.
56. Jolley, K. A.,, R. J. Russell,, D. W. Hough, and, M. J. Danson. 1997. Site-directed mutagenesis and halophilic-ity of dihydrolipoamide dehydrogenase from the halophilic archaeon, Haloferax volcanii. Eur. J. Biochem. 248:362368.
57. Kaczowka, S. J.,, C. J. Reuter,, L. A. Talarico, and, J. A. Maupin-Furlow. 2005. Recombinant production of Zymomonas mobilis pyruvate decarboxylase in the haloar-chaeon Haloferax volcanii. Archaea 1:327334.
58. Kalyuzhnaya, M. G.,, A. Lapidus,, N. Ivanova,, A.C. Copeland,, A. C. McHardy,, E. Szeto,, A. Salamov,, I. V. Grigoriev,, D. Suciu,, S. R. Levine,, V. M. Markowitz,, I. Rigoutsos,, S. G. Tringe,, D. C. Bruce,, P. M. Richardson,, M. E Lidstrom, and, L. Chistoserdova. 2008. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat. Biotechnol. 26:10291034.
59. Kashima, Y.,, K. Mori,, H. Fukada, and, K. Ishikawa. 2005. Analysis of the function of a hyperthermophilic endoglucanase from Pyrococcus horikoshii that hydrolyzes crystalline cellulose. Extremophiles 9:3743.
60. Kiiskinen, L.-L.,, L. Viikari, and, K. Kruuk. 2002. Purification and characterisation of a novel laccase from the ascomycete Melanocarpus albomyces. Appl. Microbiol. Biotechnol. 59:198204.
61. Kobayashi, H.,, A. Kuwae,, H. Maseda,, A. Nakamura, and, T. Hoshino. 2005. Isolation of a low-molecular-weight, multicopy plasmid, pNHK101, from Thermus sp. TK10 and its use as an expression vector for T. thermophilus HB27. Plasmid 54:7079.
62. Lam, W. L., and, W. F. Doolittle. 1992. Mevinolin-resistant mutations identify a promoter and the gene for a eukaryote-like 3-hydroxy-3-methylglutaryl-coenzyme A reductase in the archaebacterium Haloferax volcanii. J. Biol. Chem. 267:58295834.
63. Lasa, I.,, M. de Grado,, M. A. de Pedro, and, J. Berenguer. 1992. Development of Thermus-Escherichia shuttle vectors and their use for expression of the Clostridium thermocel-lum celA gene in Thermus thermophilus. J. Bacteriol. 174:64246431.
64. Li, D.-C.,, M. Lu,, Y.-L. Li, and, J. Lu, 2003. Purification and characterization of an endocellulase from the ther-mophilic fungus Chaetomium thermophilum CT2. Enzyme Microb. Technol. 33:932937.
65. Lodha, S. J.,, A. R. Korus, and, D. L. Crawford. 1991. Synthesis and properties of lignin peroxidases from Streptomycetes viridosporus T7A. Appl. Biochem. Biotechnol. 28:411420.
66. Lucas, S.,, L. Toffin,, Y. Zivanovic,, D. Charlier,, H. Moussard,, P. Forterre,, D. Prieur, and, G. Erauso. 2002. Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi. Appl. Environ. Microbiol. 68:55285536.
67. Lynd, L.R.,, W. H. van Zyl,, J. E. McBride, and, M. Laser. 2005. Consolidated bioprocessing of cellulosic biomass: an update. Curr. Opin. Biotechnol. 16:577583.
68. Madigan, M. T.,, J. M. Martinko, and, J. Parker. 2000. Brock Biology of Microorganisms, 9th ed. Prentice Hall International Inc., London, United Kingdom.
69. Martinez, A.,, S. J. Kolvek,, C. L. Yip,, J. Hopke,, K. A. Brown,, I. A. MacNeil, and, M. S. Osburne. 2004. Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts. Appl. Environ. Microbiol. 70:24522463.
70. Masui, R.,, K. Kurokawa,, N. Nakagawa,, F. Tokunaga,, Y. Koyama,, T. Shibata,, T. Oshima,, S. Yokoyama,, T. Yasunaga, and, S. Kuramitsu. 2005. Thermus thermophilus HB8, complete genome. http://www.ncbi.nlm.nih.gov/nuccore/AP008226. (Online.) Accessed 30 April 2009.
71. Mather, M. W., and, J. A. Fee. 1992. Development of plasmid cloning vectors for Thermus thermophilus HB8: expression of a heterologous, plasmid-borne kanamycin nucleotidyltransferase gene. Appl. Environ. Microbiol. 58:421425.
72. Matsuura, T.,, K. Miyai,, S. Trakulnaleamsai,, T. Yomo,, Y. Shima,, S. Miki,, K. Yamamoto, and, I. Urabe. 1999. Evolutionary molecular engineering by random elongation mutagenesis. Nat. Biotechnol. 17:5861.
73. Mevarech, M.,, F. Frolow, and, L. M. Gloss. 2000. Halo-philic enzymes: proteins with a grain of salt. Biophys. Chem. 86:155164.
74. Miller, G. 1959. Use of dinitrosalisylic acid reagent for determination of reducing sugar. Anal. Chem. 31:426428.
75. Moreno, R.,, A. Haro,, A. Castellanos, and, J. Berenguer. 2005. High-level overproduction of His-tagged Tth DNA polymerase in Thermus thermophilus. Appl. Environ. Microbiol. 71:591593.
76. Moreno, R.,, O. Zafra,, F. Cava, and, J. Berenguer. 2003. Development of a gene expression vector for Thermus ther-mophilus based on the promoter of the respiratory nitrate reductase. Plasmid 49:28.
77. Morita, P. 1975. Psychrophilic bacteria. Bacteriol. Rev. 39:144167.
78. Nesper, J.,, A. Brosig,, P. Ringler,, G. J. Patel,, S. A. Muller,, J. H. Kleinschmidt,, W. Boos,, K. Diederichs, and, W. Welte. 2008. Omp85(Tt) from Thermus thermophilus HB27: an ancestral type of the Omp85 protein family. J. Bacteriol. 190:45684575.
79. Nieuwlandt, D. T., and, C. J. Daniels. 1990. An expression vector for the archaebacterium Haloferax volcanii. J. Bacteriol. 172:71047110.
80. Niku-Paavola, M.-L.,, E. Karhunen,, P. Salola, and, V. Raunio. 1988. Ligninolytic enzymes of the white-rot fungus Phlebia radiata. Biochem. J. 254:877884.
81. Norris, P. R., and, D. B. Johnson. 1998. Acidophilic microorganisms, p. 133154. In K. Horikoshi and, W. D. Grant (ed.), Extremophiles—Microbial Life in Extreme Environments. Wiley-Liss Inc., New York, NY.
82. Oren, A. 2002. Halophilic Microorganisms and Their Environments. Springer, Berlin, Germany.
83. Parekh, S. R.,, S. Yu, and, M. Wayman. 1989. Adaptation of Candida shehatae and Pichia stipitis to wood hydrolysates for increased ethanol production. Appl. Microbiol. Biotechnol. 25:300304.
84. Park, H. S.,, K. J. Kayser,, J. H. Kwak, and, J. J. Kilbane II. 2004. Heterologous gene expression in Thermus ther-mophilus: beta-galactosidase, dibenzothiophene monooxy-genase, PNB carboxy esterase, 2-aminobiphenyl-2,3-diol dioxygenase, and chloramphenicol acetyl transferase. J. Ind. Microbiol. Biotechnol. 31:189197.
85. Pfeifer, F.,, S. Offner,, K. Krüger,, P. Ghahraman, and, C. Englert. 1994. Transformation of halophilic archaea and investigation of gas-vesicle synthesis. Syst. Appl. Microbiol. 16:569577.
86. Prieur, D.,, G. Erauso,, C. Geslin,, S. Lucas,, M. Gaillard,, A. Bidault,, A. C. Mattenet,, K. Rouault,, D. Flament,, P. Forterre, and, M. Le Romancer. 2004. Genetic elements of Thermococcales. Biochem. Soc. Trans. 32:184187.
87. Russell, N. J., and, T. Hamamoto. 1998. Psychrophiles, p. 2546. In K. Horikoshi and, W. D. Grant (ed.), Extremo-philes—Microbial Life in Extreme Environments. Wiley-Liss Inc., New York, NY.
88. Saboulard, D.,, V. Dugas,, M. Jaber,, J. Broutin,, E. Souteyrand,, J. Sylvestre, and, M. Delcourt. 2005. High-throughput site-directed mutagenesis using oligonucleotides synthesized on DNA chips. Biotechniques 39:363368.
89. Santangelo, T. J.,, L. Cubonova, and, J. N. Reeve. 2008. Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl. Environ. Microbiol. 74:30993104.
90. Schleper, C.,, K. Kubo, and, W. Zillig. 1992. The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral DNA. Proc. Natl. Acad. Sci. USA 89:76457649.
91. Schwarzenlander, C., and, B. Averhoff. 2006. Characterization of DNA transport in the thermophilic bacterium Thermus thermophilus HB27. FEBS J. 273:42104218.
92. Serour, E., and, G. Antranikian. 2002. Novel thermoactive glucoamylases from the thermoacidophilic Archaea Thermoplasma acidophilum, Picrophilus torridus and Picrophi-lus oshimae. Antonie van Leeuwenhoek 81:7383.
93. She, Q.,, R. K. Singh,, F. Confalonieri,, Y. Zivanovic,, G. Allard,, M. J. Awayez,, C. C. Chan-Weiher,, I. G. Clausen,, B. A. Curtis,, A. De Moors,, G. Erauso,, C. Fletcher,, P. M. Gordon,, I. Heikamp-de Jong,, A. C. Jeffries,, C. J. Kozera,, N. Medina,, X. Peng,, H. P. Thi-Ngoc,, P. Redder,, M. E. Schenk,, C. Theriault,, N. Tolstrup,, R. L. Charlebois,, W. F. Doolittle,, M. Duguet,, T. Gaasterland,, R. A. Garrett,, M. A. Ragan,, C. W. Sensen, and, J. Van der Oost. 2001. The complete genome of the crenarchaeon Sulfolobus solfa- taricus P2. Proc. Natl. Acad. Sci. USA 98:78357840.
94. Singh, S. K., and, P. C. Banerjee. 2007. Nucleotide sequence analysis of cryptic plasmid pAM5 from Acidiphilium multivorum. Plasmid 58:101114.
95. Sivakumar, N.,, N. Lia,, J. W. Tang,, B. K. C. Patel, and, K. Swaminathan. 2006. Crystal structure of AmyA lacks acidic surface and provide insights into protein stability at poly-extreme condition. FEBS Lett. 580:26462652.
96. Sommer, P.,, T. Georgieva, and, B. K. Ahring. 2004. Potential for using thermophilic anaerobic bacteria for bioethanol production from hemicellulose. Biochem. Soc. Trans. 32:283289.
97. Staskawicz, B.,, D. Dahlbeck,, N. Keen, and, C. Napoli. 1987. Molecular characterization of cloned avirulence genes from race 0 and race 1 of Pseudomonas syringae pv. glycinea. J. Bacteriol. 169:57895794.
98. Stephens, D. E.,, K. Rumbold,, K. Permaul,, B. A. Prior, and, S. Singh. 2007. Directed evolution of the thermostable xylanase from Thermomyces lanuginosus. J. Biotechnol. 127:348354.
99. Stetter, K. O. 1998. Hyperthermophiles: isolation, classification and properties, p. 124. In K. Horikoshi and, W. D. Grant (ed.), Extremophiles—Microbial Life in Extreme Environments. Wiley-Liss Inc., New York, NY.
100. Stewart, B. J., and, J. M. Leatherwood. 1976. Dere-pressed synthesis of cellulase by Cellulomonas. J. Bacteriol. 128:609615.
101. Taylor, M. P.,, C. D. Esteban, and, D. J. Leak. 2008. Development of a versatile shuttle vector for gene expression in Geobacillus spp. Plasmid 60:4552.
102. Techapun, C.,, N. Poosaran,, M. Watanabe, and, K. Sasaki. 2003. Thermostable and alkaline-tolerant microbial cellulase-free xylanases produced from agricultural wastes and the properties required for use in pulp bleaching bioprocesses: a review. Process Biochem. 38:13271340.
103. Tuncer, M,, A. S. Ball,, A. Rob, and, M. T. Wilson. 1999. Optimization of extracellular lignocellulolytic enzyme production by a thermophilic actinomycete Thermomonospora fusca BD25. Enzyme Microb. Technol. 25:3847.
104. Van Zyl, C.,, B. A. Prior, and, J. C. du Preez. 1991. Acetic acid inhibition of d-xylose fermentation by Pichia stipitis. Enzyme Microb. Technol. 13:8286.
105. Venter, J. C.,, K. Remington,, J. F. Heidelberg,, A. L. Halpern,, D. Rusch,, J. A. Eisen,, D. Wu,, I. Paulsen,, K. E. Nelson,, W. Nelson,, D. E. Fouts,, S. Levy,, A. H. Knap,, M. W. Lomas,, K. Nealson,, O. White,, J. Peterson,, J. Hoffman,, R. Parsons,, H. Baden-Tillson,, C. Pfannkoch,, Y. H. Rogers, and, H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:6674.
106. Vieites, J. M.,, M. E. Guazzaroni,, A. Beloqui,, P. N. Golyshin, and, M. Ferrer. 2008. Metagenomics approaches in systems microbiology. FEMS Microbiol. Rev. 33:236255.
107. Wendoloski, D.,, C. Ferrer, and, M. L. Dyall-Smith. 2001. A new simvastatin (mevinolin)-resistance marker from Haloarcula hispanica and a new Haloferax volca-nii strain cured of plasmid pHV2. Microbiology 147:959964.
108. Wenzel, S. C., and, R. Muller. 2005. Recent developments towards the heterologous expression of complex bacterial natural product biosynthetic pathways. Curr. Opin. Biotechnol. 16:594606.
109. Yu, W.-H.,, S.-C. Su, and, C.-Y. Lee. 2008. A novel retrieval system for nearly complete microbial genomic fragments from soil samples. J. Microbiol. Methods 72:197205.

Tables

Generic image for table
TABLE 1

Useful pH range of common biological buffers (25°C, 0.1 M)

Citation: Cowan D, Kirby B, Meiring T, Ferrer M, Guazzaroni M, Golyshina O, Golyshin P. 2010. Enzymes from Extreme Environments, p 43-61. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch4
Generic image for table
TABLE 2

Trizma buffer: pH versus temperature

Citation: Cowan D, Kirby B, Meiring T, Ferrer M, Guazzaroni M, Golyshina O, Golyshin P. 2010. Enzymes from Extreme Environments, p 43-61. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch4
Generic image for table
TABLE 3

Lignocellulosic-degrading enzymes produced by extremophiles: producing strains and assays used

Citation: Cowan D, Kirby B, Meiring T, Ferrer M, Guazzaroni M, Golyshina O, Golyshin P. 2010. Enzymes from Extreme Environments, p 43-61. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch4

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error