Extremophile Laboratory Publications

• Cavicchioli, R. (Ed). 2007. Archaea: Molecular and Cellular Biology. ASM Press, Washington, DC, USA. (23 chapters, 556 pages) ISBN: 978-1-55581-391-8. http://estore.asm.org/viewItemDetails.asp?ItemID=673
  
  
• Thomas, T., Egan, S., Burg, D., Ng, C., Ting, L. and Cavicchioli, R. 2007. The integration of genomics and proteomics into marine, microbial ecology. Theme series on “Genomics, proteomics and metabolomics in marine ecology”. Marine Ecology Progress Series 332: 291–299.
  
  
• Cavicchioli, R., DeMaere, M. and Thomas, T. 2007. Metagenomic studies reveal the critical and wide-ranging ecological importance of uncultivated archaea: the role of ammonia oxidizers. BioEssays 29: 11–14.
  
  
• Reid, I. N., Sparks, W. B., Lubow, S., McGrath, M., Livio, M., Valenti, J., Sowers, K. R., Shukla, H. D., MacAuley, S., Miller, T., Suvanasuthi, R., Belas, R., Colman, A., Robb, F. T., DasSarma, P., Muller, J. A., Coker, J. A., Cavicchioli, R., Chen, F., DasSarma, S. 2006.  Terrestrial models for extraterrestrial life: methanogens and halophiles at Martian temperatures. International Journal of Astrobiology 5: 89-97.
  
  
• Cavicchioli, R. 2006. Cold adapted Archaea. Nature Reviews Microbiology 4: 331-343.
  
  
• Siddiqui, K.S. and Cavicchioli, R. 2006. Cold adapted enzymes. Annual Review of Biochemistry 75: 403-433.
  
  
• Saunders, N. F. W., Ng, C., Raftery, M., Guilhaus, M., Goodchild, A. and Cavicchioli, R. 2006. Proteomic and computational analysis of secreted proteins with type I signal peptides from the Antarctic archaeon Methanococcoides burtonii. Journal of Proteome Research 5: 2457-2464.
  
  
• Siddiqui, K.S., Poljak, A., Guilhaus, M., De Francisci, D., Curmi, P.M.G., Feller, G., D’Amico, S., Gerday, C., Uversky, V.N., Cavicchioli, R. 2006. The role of lysine versus arginine in enzyme cold-adaptation: modifying lysine to homo-arginine stabilizes the cold-adapted a-amylase from Pseudoalteramonas haloplanktis. Proteins: Structure, Function and Bioinformatics 64: 486-501.
  
  
• Cavicchioli, R., Goodchild, A. and Raftery, M. 2006. Proteomics of archaea (Chapter 5). In, Microbial Proteomics - Functional Biology of Whole Organisms, Editors: Humphery-Smith, I. and Hecker, M., Wiley, pp. 57-72, New York.
   
• Cavicchioli, R., Curmi, P.M.G., Siddiqui, K.S. and Thomas, T. 2006. Proteins from psychrophiles (Chapter 17). In, Methods in Microbiology - Extremophiles, vol. 35, pp. 395-436. Editors: Rainey, F. A. and Oren, A., Elsevier - Academic Press, London.
  
  
• Cavicchioli, R. and Siddiqui, K.S. 2006. Cold adapted enzymes (Chapter 31). In, Enzyme Technology, Editors- Ashok Pandey, C Webb, CR Soccol & C Larroche, pp. 615-638, Springer Science, New York, USA.
  
  
• Siddiqui, K.S., Poljak, A., Guilhaus, M., Feller, G., D’Amico, S., Gerday, C. and Cavicchioli, R. 2005. The role of disulfide-bridges in the activity and stability of a cold-active alpha-amylase. Journal of Bacteriology 187: 6206–6212.
  
   
• Siddiqui, K.S., Giaquinto, L., Feller, G., D’Amico, S., Gerday, C. and Cavicchioli, R. 2005. The active site is the least stable structure in the unfolding pathway of a multi-domain cold-adapted alpha-amylase. Journal of Bacteriology 187: 6197–6205.
  
  
• Siddiqui, K.S. and Cavicchioli, R. 2005. Improved thermal stability and activity in the cold-adapted lipase B from Candida antarctica following chemical modification with oxidized polysaccharides. Extremophiles 9: 471–476.
  
  
• Saunders, N.F.W., Goodchild, A., Raftery, M., Guilhaus, M., Curmi, P.M.G. and Cavicchioli, R. 2005. Predicted Roles for Hypothetical Proteins in the Low-Temperature Expressed Proteome of the Antarctic Archaeon Methanococcoides burtonii. Journal of Proteome Research 4: 464-472.
  
  
• Goodchild, A., Raftery, M., Saunders, N.F.W., Guilhaus, M. and Cavicchioli, R. 2005. Cold Adaptation of the Antarctic Archaeon, Methanococcoides burtonii Assessed by Proteomics Using ICAT. Journal of Proteome Research 4: 473-480.
  
  
• Goodchild, A., Raftery, M., Saunders, N.W., Guilhaus, M. and Cavicchioli, R. 2004. The biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry. Journal of Proteome Research 3: 1164-1176.
  
  
• Nichols, D., Miller, M.R., Davies, N.W., Goodchild, A., Raftery, M. and Cavicchioli, R. 2004. Cold adaptation in the Antarctic archaeon, Methanococcoides burtonii, involves membrane lipid unsaturation. Journal of Bacteriology 186: 8508-8515.
  
  
• Cavicchioli, R. and Siddiqui, K.S. 2004. Cold adapted enzymes (Chapter 31). In, Enzyme Technology, Eds. Pandey, A., Webb, C., Soccol, C.R. and Larroche, C. pp 615-638, Asiatech Publishers, Inc., New Delhi, India.ISBN 81-78680-12-1
  
  
• Siddiqui, K.S., Poljak, A. and Cavicchioli, R. 2004. Improved activity and stability of alkaline phosphatases from psychrophilic and mesophilic organisms by chemically modifying aliphatic or amino groups using tetracarboxy-benzophenone derivatives. Special Issue on "Microbes from Cold Habitats: Biodiversity, Biotechnology and Cold Adaptation" in Cellular and Molecular Biology. 50: 657-667
  
  
• Roberts, T.H., Hejgaard, J., Saunders N.F.W., Cavicchioli, R. and Curmi, P.M.G. 2004. Serpins in Archaea, Bacteria and unicellular Eukarya: sequence analysis and evolution. Journal of Molecular Evolution. 59: 437-447.
  
  
• Saunders, N.F.W., Curmi, P.M.G. and Cavicchioli, R. 2004. Detection of novel archaeal sequences in the human EST database. Bioinformatics. 20: 2361-2362.
  
  
• Goodchild, A., Saunders, F.W., Ertan, H., Raftery, M., Guilhaus, M., Curmi, P.M.G. and Cavicchioli, R. 2004. A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii. Molecular Microbiology 53: 309-321.
  
  
• Ostrowski, M., Fegatella, F., Wasinger, V., Corthals, G., Guilhaus, M. and Cavicchioli, R. 2004. Cross species identification of proteins from proteome profiles of the marine oligotrophic ultramicrobacterium, Sphingopyxis alaskensis. Proteomics. 4: 1779-1788.
  
  
• Cavicchioli, R. and Thomas, T. 2004. Extremophiles. In, Schaechter M (Ed). The Desk Encyclopedia of Microbiology pp. 434-451, Elsevier, London.
  
  
• Caviccchioli, R. and Curmi, P.M.G. 2004. Response to Martin, W. Pathogenic archaea: Do they not exist because archaea use different vitamins? BioEssays 26: 592-593.
  
  
• Cavicchioli, R., Curmi, P.M.G., Saunders, N. and Thomas, T. 2003. Pathogenic archaea: do they exist? BioEssays 25: 1119-1128.
  
  
• Noon, K.R., Guymon, R., Crain, P.F., McCloskey, J.A., Thomm, M., Lim, J. and Cavicchioli, R. 2003. Influence of temperature on tRNA modification in Archaea: Methanococcoides burtonii (Topt 23°C) and Stetteria hydrogenophila (Topt 90°C). Journal of Bacteriology 185: 5483-5490.
  
  
• Saunders, N., Thomas, T., Curmi, P.M.G., Mattick, J.S., Kuczek, E., Slade, R., Davis, J., Franzmann, P.D., Boone, D., Rusterholtz, K., Feldman, R., Gates, C., Bench, S., Sowers, K., Kadner, K., Aerts, A., Dehal, P., Detter, C., Glavina, T., Lucas, S., Richardson, P., Larimer, F., Hauser, L., Land, M. and Cavicchioli, R. 2003. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea, Methanogenium frigidum and Methanococcoides burtonii. Genome Research 13: 1580-1588.
  
  
• Cavicchioli, R., Ostrowski, M., Fegatella, F., Goodchild, A. and Guixa-Boixereu, N. 2003. Life under nutrient limitation in oligotrophic marine environments: an eco/physiological perspective of Sphingopyxis alaskensis (formerly Sphingomonas alaskensis). Microbial Ecology 45: 203-217.
  
  
• Cavicchioli, R. and Ostrowski, M. 2003. Ultramicrobacteria. In, Nature Encyclopedia of Life Sciences, Nature Publishing Group (http://www.els.net), London.
  
  
• Cavicchioli, R. 2002. Extremophiles and the search for extra-terrestrial life. Astrobiology 2: 281-292.
  
  
• Cavicchioli, R., Siddiqui, K.S., Andrews, D. and Sowers, K.R. 2002. Low-temperature extremophiles and their applications. Current Opinion in Biotechnolgy 13: 253-261.
  
  
• Thomas, T. and Cavicchioli, R. 2002. Cold adaptation of archaeal elongation factor 2 (EF-2) proteins. Current Protein and Peptide Science. 3: 223-230.
  
  
• Siddiqui, K.S., Cavicchioli, R. and Thomas, T. 2002. Thermodynamic activation properties of elongation factor 2 (EF-2) proteins from psychrotolerant and thermophilic archaea. Extremophiles 6: 143-150.
  
  
• Cavicchioli, R., Saunders, N. and Thomas, T. 2002. Cold shock response in microorganisms, in Extremophiles, in Encyclopedia of Life Support Systems (EOLSS), Eolss publishers, Oxford, UK (http://www.eolss.net/)
  
  
• Thomas, T., Kumar, N. and Cavicchioli, R. 2001. Effects of ribosomes and intracellular solutes on activities and stabilities of elongation factor 2 proteins from psychrotolerant and thermophilic methanogens. Journal of Bacteriology 183: 1974-1982.
  
  
• Ostrowski, M., Cavicchioli, R., Blaauw, M. and Gottschal, J. 2001. Specific growth rate plays a critical role in hydrogen peroxide resistance of the marine oligotrophic ultramicrobacterium Sphingomonas alaskensis strain RB2256. Applied and Environmental Microbiology 67: 1292-1299.
  
  
• Eguchi, M., Ostrowski, M., Fegatella, F., Bowman, J., Nichols, D., Nishino, T. and Cavicchioli, R. 2001. Sphingomonas alaskensis, Strain AF01: an abundant oligotrophic ultramicrobacterium from the North Pacific. Applied and Environmental Microbiology 67: 4945-4954.
  
  
• Thomas, T. and Cavicchioli, R. 2000. Effect of temperature on the stability and activity of the elongation factor 2 proteins from low-temperature adapted and thermophilic methanogens. Journal of Bacteriology 182: 1328-1332.
  
  
• Lim, J., Thomas, T. and Cavicchioli, R. 2000. Low temperature regulated DEAD-box RNA helicase from the Antarctic archaeon, Methanococcoides burtonii. Journal of Molecular Biology. 297: 553-567.
  
  
• Berchet, V., Thomas, T., Cavicchioli, R., Russell , N.J. and Gounot, A.M. 2000. Structural analysis of the elongation factor G protein from the low-temperature adapted bacterium Arthrobacter globiformis SI55. Extremophiles 4: 123-130.
  
  
• Fegatella, F. and Cavicchioli, R. 2000. Physiological responses to starvation in the marine oligotrophic ultramicrobacterium, Sphingomonas sp. RB2256. Applied and Environmental Microbiology 66: 2037-2044.
  
  
• Cavicchioli, R., Thomas, T. and Curmi, P.M.G. 2000. Cold stress response in archaea. Extremophiles 4: 321-331.
  
  
• Cavicchioli, R., and Thomas, T. 2000. Extremophiles. In, Lederberg J, Alexander M, Bloom BR, Hopwood D, Hull R, Iglewski BH, Laskin AI, Oliver SG, Schaechter M, Summers WC (eds.), Encylopedia of Microbiology, 2nd edition. pp. 317-337. Academic Press Inc., San Diego.
  
  
• Fegatella, F. and Cavicchioli, R. 2000. Sphingomonas alaskensis RB2256, a novel marine oligotrophic ultramicrobacterium. pp. 93-101. Hardjito, L. (Ed) Proceedings of the International Symposium on Marine Biotechnology: The role of Marine Biotechnology in the Third Millenium. May 29-31, Ancol, Jakarta. Center for Coastal and Marine Resources Studies, Bogor Agricultural Institute, Indonesia (Publisher). ISBN : 979-9336-09-0.
  
  
• Fegatella, F., Ostrowski, M. and Cavicchioli, R. 1999. An assessment of protein profiles from the marine oligotrophic ultramicrobacterium, Sphingomonas sp., strain RB2256. Electrophoresis. 20: 2094-2098.
  
  
• Cavicchioli, R., Fegatella, F., Ostrowski, M., Eguchi, M. and Gottschal, J. 1999. Sphingomonads from marine environments. Journal of Industrial Microbiology and Biotechnology 23: 268-272.
  
  
• Thomas, T. and Cavicchioli, R. 1998. Archaeal cold-adapted proteins: structural and evolutionary analysis of the elongation factor 2 proteins from psychrophilic, mesophilic and thermophilic methanogens. FEBS Letters 439: 281-286.
  
  
• Fegatella, F., Lim, J., Kjelleberg, S. and Cavicchioli, R. 1998. Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium, Sphingomonas sp., strain RB2256. Applied and Environmental Microbiology 64: 4433-4438.
  
  
• Chiang, R., Cavicchioli, R. and Gunsalus, R.P. 1997. “Locked-on” and “Locked-off” signal transduction mutants of Escherichia coli NarQ and NarX sensors for nitrate and nitrite: role of the P-box element. Molecular Microbiology 24: 1049-1060.
  
  
• Cavicchioli, R., Kolesnikow, T., Chaing, R.C. and Gunsalus. R.P. 1996. Characterisation of the aegA locus of Escherichial coli: Control of gene expression in response to anaerobiosis and nitrate. Journal of Bacteriology 178: 6968-6974.
  
  
• Eguchi, M., Nishikawa, M., MacDonald, K., Cavicchioli, R., Gottschal, J.C. and Kjelleberg, S. 1996. Responses to stress and nutrient availability by the marine ultramicrobacterium, Sphingomonas sp. strain RB2256. Applied and Environmental Microbiology 62: 1287-1294.
  
  
• Cavicchioli, R., Chaing, R.C., Kalman, L.V., and Gunsalus, R.P. 1996. Role of the periplasmic domain of the Escherichia coli NarX sensor-transmitter protein in nitrate-dependent signal transduction and gene regulation. Molecular Microbiology 21:901-911.
  
  
• Cavicchioli, R., Schröder, I., Constanti, M., and Gunsalus. R.P. 1995. The NarX and NarQ Sensor-Transmitter proteins of Escherichia coli each require two conserved histidines for nitrate-dependent signal transduction to NarL. Journal of Bacteriology 177: 2416-2424.
  
  
• Schröder, I, Wolin, C.D., Cavicchioli, R., and Gunsalus. R.P. 1994. Phosphorylation and dephosphorylation of the NarQ, NarX and NarL proteins of the nitrate-dependent two-component regulatory system of Escherichia coli. Journal of Bacteriology 176: 4985-4992.
  
  
• Chaing, R.C., Cavicchioli, R., and Gunsalus, R.P. 1992. Identification and characterisation of narQ, a second nitrate sensor for nitrate-dependent gene regulation in Escherichia coli. Molecular Microbiology 6: 1913-1923.
  
  
• Chaing, R.C., Cavicchioli, R., and Gunsalus, R.P. 1992. Physical map location of the narQ gene of Escherichia coli. Journal of Bacteriology 174: 7882.
  
  
• Cavicchioli, R., and Watson, K. 1991. Molecular cloning, expression and characterisation of endoglucanase genes from Fibrobacter succinogenes AR1. Applied and Environmental Microbiology 57: 359-365.
  
  
• Cavicchioli, R., East, P.D., and Watson, K. 1991. FSendA, a novel family E endoglucanase gene from Fibrobacter succinogenes AR1. Journal of Bacteriology 173: 3265-3268.
  
  
• Cavicchioli, R., and Watson, K. 1991. The involvement of transcriptional read-through from internal promoters in the expression of a novel endoglucanase gene FSendA, from Fibrobacter succinogenes AR1. Nucleic Acids Research 19: 1661-1669.
  
  
• Cavicchioli, R., Lai, D. H-L. and Watson, K. 1989. Cloning and expression of cellulase genes from Bacteroides succinogenes. In, Proceedings of the 8th Australian Biotechnology Conference, Sleigh, M. (ed.). Sydney: Australian Biotechnology Association. pp. 153-156.
  
  
• Cavicchioli, R. and Watson, K., 1986. Loss of heat shock acquisition of thermotolerance in yeast is not correlated with the loss of heat shock proteins. FEBS Letters 207: 149-152.
  
  
• Watson, K., Cavicchioli, R. and Dunlop, G., 1985. Primary and secondary heat shock induction of thermal and ethanol tolerance in yeast. In, Proceedings of the 18th Convention Australian and New Zealand Institute of Brewing. Peacock publications. pp. 229-234.
  
  
• Watson, K., Dunlop, G. and Cavicchioli, R., 1984. Mitochondrial and cytoplasmic protein syntheses are not required for heat shock acquisition of ethanol and thermotolerance in yeast. FEBS Letters 172: 299-302.
  
  
• Watson, K. and Cavicchioli, R., 1983. Acquisition of ethanol tolerance in yeast cells by heat shock. Biotechnology Letters 5: 683-688.