Hot transcriptomics

Archaea

Volumn 2010, Issue , 2010, Pages

  Van Der Oost, John ^a   Walther, Jasper ^a   Sierocinski, Pawel ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA;

EID: 79953294764     PISSN: 14723646     EISSN: None     Source Type: Journal    
DOI: 10.1155/2010/897585     Document Type: Article

References (132)

1. Brock T. D., Freeze H., Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile Journal of Bacteriology 1969 98 1 289 297
2. Stetter K. O., Hyperthermophiles in the history of life Philosophical Transactions of the Royal Society B 2006 361 1474 1837 1842 (Pubitemid 44580387)
3. Angelov A., Liebl W., Insights into extreme thermoacidophily based on genome analysis of Picrophilus torridus and other thermoacidophilic archaea Journal of Biotechnology 2006 126 1 3 10 (Pubitemid 44402767)
4. Segerer A. H., Burggraf S., Fiala G., Huber G., Huber R., Pley U., Stetter K. O., Life in hot springs and hydrothermal vents Origins of Life and Evolution of the Biosphere 1993 23 1 77 90
5. Ettema T. J. G., de Vos W. M., van der Oost J., Discovering novel biology by in silico archaeology Nature Reviews Microbiology 2005 3 11 859 869 (Pubitemid 41693181)
6. Makarova K. S., Koonin E. V., Comparative genomics of archaea: how much have we learned in six years, and what's next? Genome Biology 2003 4 8, article 115
7. Brouns S. J. J., Walther J., Snijders A. P. L., Van De Werken H. J. G., Willemen H. L. D. M., Worm P., De Vos M. G. J., Andersson A., Lundgren M., Mazon H. F. M., Van Den Heuvel R. H. H., Nilsson P., Salmon L., De Vos W. M., Wright P. C., Bernander R., Van Der Oost J., Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment Journal of Biological Chemistry 2006 281 37 27378 27388 (Pubitemid 44401765)
8. Cambillau C., Claverie J. M., Structural and genomic correlates of hyperthermostability Journal of Biological Chemistry 2000 275 42 32383 32386
9. Koutsopoulos S., Van Der Oost J., Norde W., Kinetically controlled refolding of a heat-denatured hyperthermostable protein FEBS Journal 2007 274 22 5915 5923 (Pubitemid 350045803)
10. Kumar S., Nussinov R., How do thermophilic proteins deal with heat? Cellular and Molecular Life Sciences 2001 58 9 1216 1233 (Pubitemid 32844095)
11. Rivera M. C., Lake J. A., The ring of life provides evidence for a genome fusion origin of eukaryotes Nature 2004 431 7005 152 155 (Pubitemid 39243461)
12. Bult C. J., White O., Olsen G. J., Zhou L., Fleischmann R. D., Sutton G. G., Blake J. A., FitzGerald L. M., Clayton R. A., Gocayne J. D., Kerlavage A. R., Dougherty B. A., Tomb J. F., Adams M. D., Reich C. I., Overbeek R., Kirkness E. F., Weinstock K. G., Merrick J. M., Glodek A., Scott J. L., Geoghagen N. S. M., Weidman J. F., Fuhrmann J. L., Nguyen D., Utterback T. R., Kelley J. M., Peterson J. D., Sadow P. W., Hanna M. C., Cotton M. D., Roberts K. M., Hurst M. A., Kaine B. P., Borodovsky M., Klenk H. P., Fraser C. M., Smith H. O., Woese C. R., Venter J. C., Complete genome sequence of the Methanogenic archaeon, Methanococcus jannaschii Science 1996 273 5278 1058 1073 (Pubitemid 26278157)
13. Nelson K. E., Clayton R. A., Gill S. R., Gwinn M. L., Dodson R. J., Haft D. H., Hickey E. K., Peterson J. D., Nelson W. C., Ketchum K. A., McDonald L., Utterback T. R., Malek J. A., Linher K. D., Garrett M. M., Stewart A. M., Cotton M. D., Pratt M. S., Phillips C. A., Richardson D., Heidelberg J., Sutton G. G., Fleischmann R. D., Eisen J. A., White O., Salzberg S. L., Smith H. O., Venter J. C., Fraser C. M., Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima Nature 1999 399 6734 323 329 (Pubitemid 29318123)
14. Koonin E. V., Wolf Y. I., Aravind L., Prediction of the archeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach Genome Research 2001 11 2 240 252 (Pubitemid 32166533)
15. Ettema T., Van der Oost J., Huynen M., Modularity in the gain and loss of genes: applications for function prediction Trends in Genetics 2001 17 9 485 487 (Pubitemid 32763039)
16. Frickey T., Lupas A. N., PhyloGenie: automated phylome generation and analysis Nucleic Acids Research 2004 32 17 5231 5238 (Pubitemid 39445511)
17. Ruepp A., Graml W., Santos-Martinez M. L., Koretke K. K., Volker C., Mewes H. W., Frishman D., Stocker S., Lupas A. N., Baumeister W., The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum Nature 2000 407 6803 508 513
18. Doerks T., von Mering C., Bork P., Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes Nucleic Acids Research 2004 32 21 6321 6326 (Pubitemid 40202090)
19. Ramsay G., DNA chips: state-of-the art Nature Biotechnology 1998 16 1 40 44 (Pubitemid 28035946)
20. Lundgren M., Bernander R., Genome-wide transcription map of an archaeal cell cycle Proceedings of the National Academy of Sciences of the United States of America 2007 104 8 2939 2944 (Pubitemid 46327982)
21. Auernik K. S., Kelly R. M., Physiological versatility of the extremely thermoacidophilic archaeon metallosphaera sedula supported by transcriptomic analysis of heterotrophic, autotrophic, and mixotrophic growth Applied and Environmental Microbiology 2010 76 3 931 935
22. Trauger S. A., Kalisak E., Kalisiak J., Morita H., Weinberg M. V., Menon A. L., Poole F. L., Adams M. W. W., Siuzdak G., Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile Journal of Proteome Research 2008 7 3 1027 1035
23. Albers S. V., Birkeland N. K., Driessen A. J. M., Gertig S., Haferkamp P., Klenk H. P., Kouril T., Manica A., Pham T. K., Ruoff P., Schleper C., Schomburg D., Sharkey K. J., Siebers B., Sierocinski P., Steuer R., van der Oost J., Westerhoff H. V., Wieloch P., Wright P. C., Zaparty M., SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation Biochemical Society Transactions 2009 37 1 58 64
24. Schut G. J., Zhou J., Adams M. W. W., DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: evidence for a new type of sulfur-reducing enzyme complex Journal of Bacteriology 2001 183 24 7027 7036 (Pubitemid 33121834)
25. Baliga N. S., Pan M., Goo Y., Yi E. C., Goodlett D. R., Dimitrov K., Shannon P., Aebersold R., Ng W. V., Hood L., Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach Proceedings of the National Academy of Sciences of the United States of America 2002 99 23 14913 14918 (Pubitemid 35334584)
26. Zaigler A., Schuster S. C., Soppa J., Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii Molecular Microbiology 2003 48 4 1089 1105 (Pubitemid 36628271)
27. Schut G. J., Brehm S. D., Datta S., Adams M. W. W., Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: pyrococcus furiosus grown on carbohydrates or peptides Journal of Bacteriology 2003 185 13 3935 3947 (Pubitemid 36735945)
28. Mller J. A., DasSarma S., Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors Journal of Bacteriology 2005 187 5 1659 1667
29. Hovey R., Lentes S., Ehrenreich A., Salmon K., Saba K., Gottschalk G., Gunsalus R. P., Deppenmeier U., DNA microarray analysis of Methanosarcina mazei G1 reveals adaptation to different methanogenic substrates Molecular Genetics and Genomics 2005 273 3 225 239 (Pubitemid 40768510)
30. Snijders A. P. L., Walther J., Peter S., Kinnman I., De Vos M. G. J., Van De Werken H. J. G., Brouns S. J. J., Van Der Oost J., Wright P. C., Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis Proteomics 2006 6 5 1518 1529
31. Culley D. E., Kovacik W. P., Brockman F. J., Zhang W., Optimization of RNA isolation from the archaebacterium Methanosarcina barkeri and validation for oligonucleotide microarray analysis Journal of Microbiological Methods 2006 67 1 36 43 (Pubitemid 44279100)
32. Veit K., Ehlers C., Ehrenreich A., Salmon K., Hovey R., Gunsalus R. P., Deppenmeier U., Schmitz R. A., Global transcriptional analysis of Methanosarcina mazei strain G1 under different nitrogen availabilities Molecular Genetics and Genomics 2006 276 1 41 55 (Pubitemid 43946093)
33. Lee H. S., Shockley K. R., Schut G. J., Conners S. B., Montero C. I., Johnson M. R., Chou C. J., Bridger S. L., Wigner N., Brehm S. D., Jenney F. E., Comfort D. A., Kelly R. M., Adams M. W. W., Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus Journal of Bacteriology 2006 188 6 2115 2125 (Pubitemid 43376465)
34. Schut G. J., Bridger S. L., Adams M. W. W., Insights into the metabolism of elemental sulfur by the hyperthermophilic archaeon Pyrococcus furiosus: characterization of a coenzyme A-dependent NAD(P)H sulfur oxidoreductase Journal of Bacteriology 2007 189 12 4431 4441 (Pubitemid 46919630)
35. Twellmeyer J., Wende A., Wolfertz J., Pfeiffer F., Panhuysen M., Zaigler A., Soppa J., Welzi G., Oesterhelt D., Microarray analysis in the archaeon Halobacterium salinarum strain R1 PLoS ONE 2007 2 10,article e1064
36. Li L., Li Q., Rohlin L., Kim U., Salmon K., Rejtar T., Gunsalus R. P., Karger B. L., Ferry J. G., Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol Journal of Proteome Research 2007 6 2 759 771 (Pubitemid 46340179)
37. Rich J. J., Dale O. R., Song B., Ward B. B., Anaerobic ammonium oxidation (anammox) in Chesapeake Bay sediments Microbial Ecology 2008 55 2 311 320 (Pubitemid 351171471)
38. Auernik K. S., Kelly R. M., Identification of components of electron transport chains in the extremely thermoacidophilic crenarchaeon Metallosphaera sedula through iron and sulfur compound oxidation transcriptomes Applied and Environmental Microbiology 2008 74 24 7723 7732
39. Ferry J. G., Lessner D. J., Methanogenesis in marine sediments Annals of the New York Academy of Sciences 2008 1125 147 157 (Pubitemid 351451153)
40. Cozen A. E., Weirauch M. T., Pollard K. S., Bernick D. L., Stuart J. M., Lowe T. M., Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum Journal of Bacteriology 2009 191 3 782 794
41. Zaparty M., Tjaden B., Hensel R., Siebers B., The central carbohydrate metabolism of the hyperthermophilic crenarchaeote Thermoproteus tenax: pathways and insights into their regulation Archives of Microbiology 2008 190 3 231 245
42. Wende A., Furtwngler K., Oesterhelt D., Phosphate-dependent behavior of the archaeon Halobacterium salinarum strain R1 Journal of Bacteriology 2009 191 12 3852 3860
43. Schmid A. K., Reiss D. J., Pan M., Koide T., Baliga N. S., A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability Molecular Systems Biology 2009 5, article 282
44. Johnsen U., Dambeck M., Zaiss H., Fuhrer T., Soppa J., Sauer U., Schnheit P., D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii Journal of Biological Chemistry 2009 284 40 27290 27303
45. Jger D., Sharma C. M., Thomsen J., Ehlers C., Vogel J., Schmitz R. A., Deep sequencing analysis of the Methanosarcina mazei G 1 transcriptome in response to nitrogen availability Proceedings of the National Academy of Sciences of the United States of America 2009 106 51 21878 21882
46. Auernik K. S., Kelly R. M., Impact of molecular hydrogen on chalcopyrite bioleaching by the extremely thermoacidophilic archaeon Metallosphaera sedala Applied and Environmental Microbiology 2010 76 8 2668 2672
47. Shockley K. R., Ward D. E., Chhabra S. R., Conners S. B., Montero C. I., Kelly R. M., Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus Applied and Environmental Microbiology 2003 69 4 2365 2371 (Pubitemid 36443659)
48. Weinberg M. V., Schut G. J., Brehm S., Datta S., Adams M. W. W., Cold shock of a hyperthermophilic archaeon: pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins Journal of Bacteriology 2005 187 1 336 348 (Pubitemid 40024210)
49. McCready S., UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp. NRC-1 Saline Systems 2005 1 3
50. Boonyaratanakornkit B. B., Simpson A. J., Whitehead T. A., Fraser C. M., El-Sayed N. M. A., Clark D. S., Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock Environmental Microbiology 2005 7 6 789 797 (Pubitemid 40697637)
51. Zhang W., Culley D. E., Nie L., Brockman F. J., DNA microarray analysis of anaerobic Methanosarcina barkeri reveals responses to heat shock and air exposure Journal of Industrial Microbiology and Biotechnology 2006 33 9 784 790 (Pubitemid 44106685)
52. Boonyaratanakornkit B., Crdova J., Park C. B., Clark D. S., Pressure affects transcription profiles of Methanocaldococcus jannaschii despite the absence of barophilic growth under gas-transfer limitation Environmental Microbiology 2006 8 11 2031 2035 (Pubitemid 44506898)
53. Williams E., Lowe T. M., Savas J., DiRuggiero J., Microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation Extremophiles 2007 11 1 19 29 (Pubitemid 46089625)
54. Pflger K., Ehrenreich A., Salmon K., Gunsalus R. P., Deppenmeier U., Gottschalk G., Mller V., Identification of genes involved in salt adaptation in the archaeon Methanosarcina mazei G1 using genome-wide gene expression profiling FEMS Microbiology Letters 2007 277 1 79 89 (Pubitemid 350045659)
55. Hendrickson E. L., Haydock A. K., Moore B. C., Whitman W. B., Leigh J. A., Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea Proceedings of the National Academy of Sciences of the United States of America 2007 104 21 8930 8934 (Pubitemid 47175414)
56. Coker J. A., DasSarma P., Kumar J., Mller J. A., DasSarma S., Transcriptional profiling of the model Archaeon Halobacterium sp. NRC-I: responses to changes in salinity and temperature Saline Systems 2007 3 1 1 17 (Pubitemid 350100632)
57. Frls S., Gordon P. M. K., Panlilio M. A., Duggin I. G., Bell S. D., Sensen C. W., Schleper C., Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage Journal of Bacteriology 2007 189 23 8708 8718 (Pubitemid 350210042)
58. Dorazi R., Gtz D., Munro S., Bernander R., White M. F., Equal rates of repair of DNA photoproducts in transcribed and non-transcribed strands in Sulfolobus solfataricus Molecular Microbiology 2007 63 2 521 529 (Pubitemid 46058937)
59. Tachdjian S., Kelly R. M., Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus Journal of Bacteriology 2006 188 12 4553 4559 (Pubitemid 43865774)
60. Simon G., Walther J., Zabeti N., Combet-Blanc Y., Auria R., Van Der Oost J., Casalot L., Effect of O concentrations on Sulfolobus solfataricus P2 FEMS Microbiology Letters 2009 299 2 255 260
61. Kirkpatrick R. D., Something old, something new, something borrowed...something blue Tennessee Medicine 2010 103 8 7 8
62. Campanaro S., Temperature-dependent global gene expression in theAntarctic archaeon Methanococcoides burtonii. Environmental Microbiology. In press
63. Kanai T., Takedomi S., Fujiwara S., Atomi H., Imanaka T., Identification of the Phr-dependent heat shock regulon in the hyperthermophilic archaeon, Thermococcus kodakaraensis Journal of Biochemistry 2010 147 3 361 370
64. Keese A. M., Schut G. J., Ouhammouch M., Adams M. W. W., Thomm M., Genome-wide identification of targets for the archaeal heat shock regulator Phr by cell-free transcription of genomic DNA Journal of Bacteriology 2010 192 5 1292 1298
65. Cooper C. R., Daugherty A. J., Tachdjian S., Blum P. H., Kelly R. M., Role of vapBC toxin-antitoxin loci in the thermal stress response of Sulfolobus solfataricus Biochemical Society Transactions 2009 37 1 123 126
66. Strand K. R., Sun C., Li T., Jenney F. E., Schut G. J., Adams M. W. W., Oxidative stress protection and the repair response to hydrogen peroxide in the hyperthermophilic archaeon Pyrococcus furiosus and in related species Archives of Microbiology 2010 192 6 447 459
67. Shih C. J., Lai M. C., Differentially expressed genes after hyper- and hypo-salt stress in the halophilic archaeon Methanohalophilus portucalensis Canadian Journal of Microbiology 2010 56 4 295 307
68. Lundgren M., Andersson A., Chen L., Nilsson P., Bernander R., Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination Proceedings of the National Academy of Sciences of the United States of America 2004 101 18 7046 7051 (Pubitemid 38596440)
69. Baumann A., Lange C., Soppa J., Transcriptome changes and cAMP oscillations in an archaeal cell cycle BMC Cell Biology 2007 8, article 21
70. Matsunaga F., Glatigny A., Mucchielli-Giorgi M. E., Agier N., Delacroix H., Marisa L., Durosay P., Ishino Y., Aggerbeck L., Forterre P., Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp Nucleic Acids Research 2007 35 10 3214 3222 (Pubitemid 47073588)
71. Stralis-Pavese N., Sessitsch A., Weilharter A., Reichenauer T., Riesing J., Csontos J., Murrell J. C., Bodrossy L., Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers Environmental Microbiology 2004 6 4 347 363 (Pubitemid 38427315)
72. Hamilton-Brehm S. D., Schut G. J., Adams M. W. W., Metabolic and evolutionary relationships among Pyrococcus species: genetic exchange within a hydrothermal vent environment Journal of Bacteriology 2005 187 21 7492 7499 (Pubitemid 41507805)
73. Andersson A. F., Lundgren M., Eriksson S., Rosenlund M., Bernander R., Nilsson P., Global analysis of mRNA stability in the archaeon Sulfolobus Genome Biology 2006 7 10, article R99
74. Xia Q., Hendrickson E. L., Zhang Y., Wang T., Taub F., Moore B. C., Porat I., Whitman W. B., Hackett M., Leigh J. A., Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR Molecular and Cellular Proteomics 2006 5 5 868 881 (Pubitemid 43792796)
75. Lange C., Zaigler A., Hammelmann M., Twellmeyer J., Raddatz G., Schuster S. C., Oesterhelt D., Soppa J., Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea BMC Genomics 2007 8, article 415
76. Kanai T., Akerboom J., Takedomi S., Van De Werken H. J. G., Blombach F., Van Der Oost J., Murakami T., Atomi H., Imanaka T., A global transcriptional regulator in Thermococcus kodakaraensis controls the expression levels of both glycolytic and gluconeogenic enzyme-encoding genes Journal of Biological Chemistry 2007 282 46 33659 33670 (Pubitemid 350159557)
77. Santangelo T. J., uboov L., Matsumi R., Atomi H., Imanaka T., Reeve J. N., Polarity in archaeal operon transcription in Thermococcus kodakaraensis Journal of Bacteriology 2008 190 6 2244 2248 (Pubitemid 351355348)
78. Dambeck M., Soppa J., Characterization of a Haloferax volcanii member of the enolase superfamily: deletion mutant construction, expression analysis, and transcriptome comparison Archives of Microbiology 2008 190 3 341 353
79. Garrido P., Gonzlez-Toril E., Garca-Moyano A., Moreno-Paz M., Amils R., Parro V., An oligonucleotide prokaryotic acidophile microarray: its validation and its use to monitor seasonal variations in extreme acidic environments with total environmental RNA Environmental Microbiology 2008 10 4 836 850 (Pubitemid 351406081)
80. Ortmann A. C., Brumfield S. K., Walther J., McInnerney K., Brouns S. J. J., Van De Werken H. J. G., Bothner B., Douglas T., Van De Oost J., Young M. J., Transcriptome analysis of infection of the archaeon Sulfolobus solfataricus with Sulfolobus turreted icosahedral virus Journal of Virology 2008 82 10 4874 4883 (Pubitemid 351657049)
81. Grogan D. W., Ozarzak M. A., Bernander R., Variation in gene content among geographically diverse Sulfolobus isolates Environmental Microbiology 2008 10 1 137 146
82. Andersson A. F., Pelve E. A., Lindeberg S., Lundgren M., Nilsson P., Bernander R., Replication-biased genome organisation in the crenarchaeon Sulfolobus BMC Genomics 2010 11 1, article 454
83. Wurtzel O., Sapra R., Chen F., Zhu Y., Simmons B. A., Sorek R., A single-base resolution map of an archaeal transcriptome Genome Research 2010 20 1 133 141
84. Yergeau E., Schoondermark-Stolk S. A., Brodie E. L., Djean S., DeSantis T. Z., Gonalves O., Piceno Y. M., Andersen G. L., Kowalchuk G. A., Environmental microarray analyses of Antarctic soil microbial communities ISME Journal 2009 3 3 340 351
85. Reichlen M. J., Murakami K. S., Ferry J. G., Functional analysis of the three TATA binding protein homologs in Methanosarcina acetivorans Journal of Bacteriology 2010 192 6 1511 1517
86. Schwaiger R., Schwarz C., Furtwngler K., Tarasov V., Wende A., Oesterhelt D., Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1 BMC Molecular Biology 2010 11, article 40
87. Facciotti M. T., Pang W. L., Lo F. Y., Whitehead K., Koide T., Masumura K. I., Pan M., Kaur A., Larsen D. J., Reiss D. J., Hoang L., Kalisiak E., Northen T., Trauger S. A., Siuzdak G., Baliga N. S., Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis BMC Systems Biology 2010 4, article 64
88. Goberna M., Gadermaier M., Garca C., Wett B., Insam H., Adaptation of methanogenic communities to the cofermentation of cattle excreta and olive mill wastes at 37 C and 55 c Applied and Environmental Microbiology 2010 76 19 6564 6571
89. Jacob Parnell J., Rompato G., Latta IV L. C., Pfrender M. E., van Nostrand J. D., He Z., Zhou J., Andersen G., Champine P., Ganesan B., Weimer B. C., Functional biogeography as evidence of gene transfer in hypersaline microbial communities PLoS ONE 2010 5 9, article e12919
90. van de Peppel J., Kemmeren P., van Bakel H., Radonjic M., van Leenen D., Holstege F. C. P., Monitoring global messenger RNA changes in externally controlled microarray experiments EMBO Reports 2003 4 4 387 393 (Pubitemid 36622004)
91. Santos H., Da Costa M. S., Compatible solutes of organisms that live in hot saline environments Environmental Microbiology 2002 4 9 501 509
92. Kagawa H. K., Yaoi T., Brocchieri L., McMillan R. A., Alton T., Trent J. D., The composition, structure and stability of a group II chaperonin are temperature regulated in a hyperthermophilic archaeon Molecular Microbiology 2003 48 1 143 156 (Pubitemid 36411473)
93. Maaty W. S. A., Ortmann A. C., Dlaki M., Schulstad K., Hilmer J. K., Liepold L., Weidenheft B., Khayat R., Douglas T., Young M. J., Bothner B., Characterization of the archaeal thermophile Sulfolobus turreted icosahedral virus validates an evolutionary link among double-stranded DNA viruses from all domains of life Journal of Virology 2006 80 15 7625 7635 (Pubitemid 44092583)
94. Palm P., Schleper C., Grampp B., Yeats S., McWilliam P., Reiter W. D., Zillig W., Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae Virology 1991 185 1 242 250
95. Ettema T. J. G., Bernander R., Cell division and the ESCRT complex: a surprise from the archaea Communitative and Integrative Biology 2009 2 2 86 88
96. Samson R. Y., Bell S. D., Ancient ESCRTs and the evolution of binary fission Trends in Microbiology 2009 17 11 507 513
97. Brumfield S. K., Ortmann A. C., Ruigrok V., Suci P., Douglas T., Young M. J., Particle assembly and ultrastructural features associated with replication of the lytic archaeal virus Sulfolobus turreted icosahedral virus Journal of Virology 2009 83 12 5964 5970
98. Bize A., Karlsson E. A., Ekefjrd K., Quax T. E. F., Pina M., Prevost M. C., Forterre P., Tenaillon O., Bernander R., Prangishvili D., A unique virus release mechanism in the Archaea Proceedings of the National Academy of Sciences of the United States of America 2009 106 27 11306 11311
99. Frls S., Gordon P. M. K., Panlilio M. A., Duggin I. G., Bell S. D., Sensen C. W., Schleper C., Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage Journal of Bacteriology 2007 189 23 8708 8718 (Pubitemid 350210042)
100. Schleper C., Kubo K., Zillig W., The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral DNA Proceedings of the National Academy of Sciences of the United States of America 1992 89 16 7645 7649
101. Johnson M. R., Conners S. B., Montero C. I., Chou C. J., Shockley K. R., Kelly R. M., The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture Applied and Environmental Microbiology 2006 72 1 811 818
102. Muralidharan V., Rinker K. D., Hirsh I. S., Bouwer E. J., Kelly R. M., Hydrogen transfer between methanogens and fermentative heterotrophs in hyperthermophilic cocultures Biotechnology and Bioengineering 1997 56 3 268 278 (Pubitemid 27440822)
103. Myllykallio H., Lopez P., Lpez-Garca P., Heilig R., Saurin W., Zivanovic Y., Philippe H., Forterre P., Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon Science 2000 288 5474 2212 2215 (Pubitemid 30429606)
104. Robinson N. P., Dionne I., Lundgren M., Marsh V. L., Bernander R., Bell S. D., Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus Cell 2004 116 1 25 38 (Pubitemid 38156181)
105. Contursi P., Pisani F. M., Grigoriev A., Cannio R., Bartolucci S., Rossi M., Identification and autonomous replication capability of a chromosomal replication origin from the archaeon Sulfolobus solfataricus Extremophiles 2004 8 5 385 391 (Pubitemid 39520726)
106. Myllykallio H., Forterre P., Mapping of a chromosome replication origin in an archaeon: response Trends in Microbiology 2000 8 12 537 539
107. Robinson N. P., Bell S. D., Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes Proceedings of the National Academy of Sciences of the United States of America 2007 104 14 5806 5811 (Pubitemid 47175615)
108. Maisnier-Patin S., Malandrin L., Birkeland N. K., Bernander R., Chromosome replication patterns in the hyperthermophilic euryarchaea Archaeoglobus fulgidus and Methanocaldococcus (Methanococcus) jannaschii Molecular Microbiology 2002 45 5 1443 1450 (Pubitemid 35015365)
109. Makarova K. S., Yutin N., Bell S. D., Koonin E. V., Evolution of diverse cell division and vesicle formation systems in Archaea Nature Reviews Microbiology 2010 8 10 731 741
110. Samson R. Y., Obita T., Freund S. M., Williams R. L., Bell S. D., A role for the ESCRT system in cell division in archaea Science 2008 322 5908 1710 1713
111. Anderson R. L., Dahms A. S., 2-Keto-3-deoxy-l-arabonate aldolase Methods in Enzymology 1975 42 269 272
112. Duggin I. G., McCallum S. A., Bell S. D., Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius Proceedings of the National Academy of Sciences of the United States of America 2008 105 43 16737 16742
113. Gtz D., Paytubi S., Munro S., Lundgren M., Bernander R., White M. F., Responses of hyperthermophilic crenarchaea to UV irradiation Genome Biology 2007 8 10, article R220
114. Mirkin B. G., Fenner T. I., Galperin M. Y., Koonin E. V., Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes BMC Evolutionary Biology 2003 3 1, article 2 2
115. Nunn C. E.M., Johnsen U., Schnheit P., Fuhrer T., Sauer U., Hough D. W., Danson M. J., Metabolism of pentose sugars in the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius Journal of Biological Chemistry 2010 285 44 33701 33709
116. van de Werken H., Brouns S., van der Oost J., Pentose metabolism in archaea Archaea: New Models for Prokaryotic Biology 2008 71
117. Berkner S., Wlodkowski A., Albers S. V., Lipps G., Inducible and constitutive promoters for genetic systems in Sulfolobus acidocaldarius Extremophiles 2010 14 3 249 259
118. Kanai T., Akerboom J., Takedomi S., Van De Werken H. J. G., Blombach F., Van Der Oost J., Murakami T., Atomi H., Imanaka T., A global transcriptional regulator in Thermococcus kodakaraensis controls the expression levels of both glycolytic and gluconeogenic enzyme-encoding genes Journal of Biological Chemistry 2007 282 46 33659 33670 (Pubitemid 350159557)
119. Margulies M., Egholm M., Altman W. E., Attiya S., Bader J. S., Bemben L. A., Berka J., Braverman M. S., Chen YI. J., Chen Z., Dewell S. B., Du L., Fierro J. M., Gomes X. V., Godwin B. C., He W., Helgesen S., Ho C. H., Irzyk G. P., Jando S. C., Alenquer M. L. I., Jarvie T. P., Jirage K. B., Kim J. B., Knight J. R., Lanza J. R., Leamon J. H., Lefkowitz S. M., Lei M., Li J., Lohman K. L., Lu H., Makhijani V. B., McDade K. E., McKenna M. P., Myers E. W., Nickerson E., Nobile J. R., Plant R., Puc B. P., Ronan M. T., Roth G. T., Sarkis G. J., Simons J. F., Simpson J. W., Srinivasan M., Tartaro K. R., Tomasz A., Vogt K. A., Volkmer G. A., Wang S. H., Wang Y., Weiner M. P., Yu P., Begley R. F., Rothberg J. M., Genome sequencing in microfabricated high-density picolitre reactors Nature 2005 437 7057 376 380 (Pubitemid 41613494)
120. Bennett S., Solexa Ltd Pharmacogenomics 2004 5 4 433 438 (Pubitemid 38923657)
121. Wilhelm B. T., Landry J. R., RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing Methods 2009 48 3 249 257
122. She Q., Singh R. K., Confalonieri F., Zivanovic Y., Allard G., Awayez M. J., Chan-Weiher C. C. Y., Clausen IB. G., Curtis B. A., De Moors A., Erauso G., Fletcher C., Gordon P. M. K., Heikamp-de Jong I., Jeffries A. C., Kozera C. J., Medina N., Peng XU., Thi-Ngoc H. P., Redder P., Schenk M. E., Theriault C., Tolstrup N., Charlebois R. L., Doolittle W. F., Duguet M., Gaasterland T., Garrett R. A., Ragan M. A., Sensen C. W., Van Der Oostg J., The complete genome of the crenarchaeon Sulfolobus solfataricus P2 Proceedings of the National Academy of Sciences of the United States of America 2001 98 14 7835 7840 (Pubitemid 32642647)
123. Waters L. S., Storz G., Regulatory RNAs in bacteria Cell 2009 136 4 615 628
124. Bonneau R., Facciotti M. T., Reiss D. J., Schmid A. K., Pan M., Kaur A., Thorsson V., Shannon P., Johnson M. H., Bare J. C., Longabaugh W., Vuthoori M., Whitehead K., Madar A., Suzuki L., Mori T., Chang D. E., DiRuggiero J., Johnson C. H., Hood L., Baliga N. S., A predictive model for transcriptional control of physiology in a free living cell Cell 2007 131 7 1354 1365 (Pubitemid 350297417)
125. Zaparty M., Esser D., Gertig S., Haferkamp P., Kouril T., Manica A., Pham T. K., Reimann J., Schreiber K., Sierocinski P., Teichmann D., van Wolferen M., von Jan M., Wieloch P., Albers S. V., Driessen A. J. M., Klenk H. P., Schleper C., Schomburg D., van der Oost J., Wright P. C., Siebers B., "Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus Extremophiles 2009 14 1 119 142
126. Booth I. R., SysMO: back to the future Nature Reviews Microbiology 2007 5 8 566 (Pubitemid 47074111)
127. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C. A., Causton H. C., Gaasterland T., Glenisson P., Holstege F. C. P., Kim I. F., Markowitz V., Matese J. C., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M., Minimum information about a microarray experiment (MIAME)toward standards for microarray data Nature Genetics 2001 29 4 365 371 (Pubitemid 34326681)
128. Mockler T. C., Ecker J. R., Applications of DNA tiling arrays for whole-genome analysis Genomics 2005 85 1 1 15 (Pubitemid 39655686)
129. Gilbert J. A., Field D., Huang Y., Edwards R., Li W., Gilna P., Joint I., Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities PLoS ONE 2008 3 8, article e3042
130. Torres T. T., Metta M., Ottenwlder B., Schltterer C., Gene expression profiling by massively parallel sequencing Genome Research 2008 18 1 172 177
131. Wang Z., Gerstein M., Snyder M., RNA-Seq: a revolutionary tool for transcriptomics Nature Reviews Genetics 2009 10 1 57 63
132. Ledford H., The death of microarrays? Nature 2008 455 7215 847