"Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus

Extremophiles

Volumn 14, Issue 1, 2009, Pages 119-142

  Zaparty, Melanie ^a   Esser, Dominik ^a   Gertig, Susanne ^b   Haferkamp, Patrick ^a   Kouril, Theresa ^a   Manica, Andrea ^c   Pham, Trong K ^d   Reimann, Julia ^e   Schreiber, Kerstin ^b   Sierocinski, Pawel ^a,f   Teichmann, Daniela ^c   van Wolferen, Marleen ^h   von Jan, Mathias ^g   Wieloch, Patricia ^b   Albers, Sonja V ^e   Driessen, Arnold J M ^h   Klenk, Hans Peter ^g   Schleper, Christa ^c,i   Schomburg, Dietmar ^b   van der Oost, John ^f   Wright, Phillip C ^d   Siebers, Bettina ^a   more..

^a UNIVERSITY OF DUISBURG ESSEN   (Germany)

^b TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^c UNIVERSITY OF VIENNA   (Austria)

^d UNIVERSITY OF SHEFFIELD   (United Kingdom)

^e MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^f WAGENINGEN UNIVERSITY   (Netherlands)

^g egene Biotechnologie GmbH   (Germany)

^h UNIVERSITY OF GRONINGEN   (Netherlands)

ⁱ UNIVERSITY OF BERGEN   (Norway)

Author keywords

Biochemistry; Crenarchaeon; Genomics; Metabolomics; Proteomics; Standard operating procedures; Systems biology; Transcriptomics

Indexed keywords

ARTICLE; GENETICS; GENOMICS; METHODOLOGY; STANDARD; SULFOLOBUS SOLFATARICUS;

GENOMICS; SULFOLOBUS SOLFATARICUS;

ARCHAEA; CRENARCHAEOTA; SULFOLOBUS; SULFOLOBUS SOLFATARICUS;

EID: 72449170468     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-009-0280-0     Document Type: Article

References (69)

1. Ahmed H, Ettema TJ, Tjaden B, Geerling AC, van der Oost J, Siebers B (2005) The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea-a re-evaluation. Biochem J 390: 529-540.
2. Albers SV, Driessen AJM (2008) Conditions for gene disruption by homologous recombination of exogenous DNA into the Sulfolobus solfataricus genome. Archaea 2: 145-149.
3. Albers SV, Elferink MGL, Charlebois RL, Sensen CW, Driessen AJM, Konings WN (1999) Glucose transport in the extremely thermoacidophilic Sulfolobus solfataricus involves a high affinity membrane-integrated binding protein. J Bacteriol 181: 4258-4291.
4. Albers SV, van de Vossenberg JLCM, Driessen AJM, Konings WN (2000) Adaptations of the archaeal cell membrane to heat stress. Front Biosci 5: 813-820.
5. Albers SV, van de Vossenberg JLCM, Driessen AJM, Konings WN (2001) Bioenergetics and solute uptake under extreme conditions. Extremophiles 5: 285-294.
6. Albers SV, Koning SM, Konings WN, Driessen AJM (2004) Insights into ABC transport in Archaea. J Bioenerg Biomembr 36: 5-15.
7. Albers SV, Jonuscheit M, Dinkelaker S, Urich T, Kletzin A Tampe R, Driessen AJM, Schleper C (2006) Production of recombinant and tagged proteins in the hyperthermophilic archaeon Sulfolobus solfataricus. Appl Environ Microbiol 72(1): 102-111.
8. Albers SV, Birkeland NK, Driessen AJM, Gertig S, Haferkamp P, Klenk HP, Kouril T, Manica A, Pham TK, Ruoff P, Schleper C, Schomburg D, Sharkey KJ, Siebers B, Sierocinski P, Steuer R, van der Oost J, Westerhoff HV, Wieloch P, Wright PC, Zaparty M (2009) SulfoSYS-Sulfolobus Systems Biology: towards a Silicon Cell Model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation. Biochem Soc Trans 37: 58-64.
9. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17): 3389-3402.
10. Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich LE, Elkins JE, Mavromatis K, Lykidis A, Kim E, Thompson LS, Nolan M, Land M, Copeland A, Lapidus A, Lucas S, Detter C, Zhulin IB, Olsen GJ, Whitman W, Mukhopadhyay B, Bristow J, Kyrpides N (2008) Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J Bacteriol 190(8): 2957-2965.
11. Andersson AF, Lundgren M, Eriksson S, Rosenlund M, Bernander R, Nilsson P (2006) Global analysis of mRNA stability in the archaeon Sulfolobus. Genome Biol 7: R99.
12. Barry ER, Bell SD (2006) DNA replication in the archaea. Microbiol Mol Biol Rev 70: 876-887.
13. Bell SD, Jackson SP (2001) Mechanism and regulation of transcription in archaea. Curr Opin Microbiol 4(2): 208-213.
14. Bisle B, Schmidt A, Scheibe B, Klein C, Tebbe A, Kellermann J, Siedler F, Pfeiffer F, Lottspeich F, Oesterhelt D (2006) Quantitative profiling of the membrane proteome in a Halophilic archaeon. Mol Cell Proteomics 5: 1543-1558.
15. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248-254.
16. Brock TD, Brock KM, Belley RT, Weiss RL (1972) Sulfolobus: a new genus of sulphur-oxidizing bacteria living at low pH and high temperature. Arch Microbiol 84: 54-68.
17. Buchanan CL, Connaris H, Danson MJ, Reeve CD, Hough DW (1999) An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for non-phosphorylated substrates. Biochem J 343: 563-570.
18. Carstens CP, Waesche A (1999) Codon bias-adjusted BL21 derivatives for protein expression strategies. Newsletter 12(2): 49-51.
19. Cava F, Hidalgo A, Berenguer J (2009) Thermus thermophilus as biological model. Extremophiles 13: 213-231.
20. Drengstig T, Ueda HR, Ruoff P (2008) Predicting perfect adaptation motifs in reaction kinetic networks. J Phys Chem B 112(51): 16752-16758.
21. Elferink MGL, Albers SV, Konings WN, Driessen AJM (2001) Sugar transport in Sulfolobus solfataricus is mediated by two families of binding protein dependent ABC transporters. Mol Microbiol 39: 1494-1503.
22. Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4: 207-214.
23. Ettema TJG, Ahmed H, Geerling ACM, van der Oost J, Siebers B (2008) The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner-Doudoroff pathway. Extremophiles 12: 75-88.
24. Fischer F, Wolters D, Rögner M, Poetsch A (2006) Toward the complete membrane proteome: high coverage of integral membrane proteins through transmembrane peptide detection. Mol Cell Proteomics 5: 444-453.
25. Fröls S, Gordon PM, Panlilio MA, Schleper C, Sensen CW (2007) Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays. Virology 365: 48-59.
26. Goncalves LG, Lamosa P, Huber R, Santos H (2008) Di-myo-inositol phosphate and novel UDP-sugars accumulate in the extreme hyperthermophile Pyrolobus fumarii. Extremophiles 12(3): 383-389.
27. Grogan DW (1989) Phenotypic characterization of the archaebacterial genus Sulfolobus: comparison of five wild-type strains. J Bacteriol 171: 6710-6719.
28. Hanahan D (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166: 557-580.
29. Jeffery CJ, Bahnson BJ, Chien W, Ringe D, Petsko GA (2000) Crystal structure of rabbit phosphoglucose isomerase, a glycolytic enzyme that moonlights as neuroleukin, autocrine motility factor, and differentiation mediator. Biochemistry 39(5): 955-964.
30. Jonuscheit M, Martusewitsch E, Stedman KM, Schleper C (2003) A reporter gene system for the hyperthermophilic archaeon Sulfolobus solfataricus based on a selectable and integrative shuttler vector. Mol Microbiol 48(5): 1241-1252.
31. Kagawa HK, Yaoi T, Brocchieri L, McMillan RA, Alton T, Trent JD (2003) The composition, structure and stability of a group II chaperonin are temperature regulated in a hyperthermophilic archaeon. Mol Microbiol 48(1): 143-156.
32. Kelman Z, White MF (2005) Archaeal DNA replication and repair. Curr Opin Microbiol 8(6): 669-676.
33. Kim S, Lee SB (2005) Identification and characterization of Sulfolobus solfataricusd-gluconate dehydratase: a key enzyme in the non-phosphorylated Entner-Doudoroff pathway. Biochem J 387: 271-280.
34. Kim S, Lee SB (2006) Catalytic promiscuity in dihydroxy-acid dehydratase from the thermoacidophilic archaeon Sulfolobus solfataricus. J Biochem 139: 591-596.
35. Lamble HJ, Heyer NI, Bull SD, Hough DW, Danson M (2003) Metabolic pathway promiscuity in the archaeon Sulfolobus solfataricus revealed by studies on glucose dehydrogenase and 2-keto-3-deoxygluconate aldolase. J Biol Chem 278(36): 34066-34072.
36. Lamble HJ, Theodossis A, Milburn CC, Taylor GL, Bull SD, Hough DW, Danson M (2005) Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett 579: 6865-6869.
37. Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC (2008) The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res 36 (Database issue): D528-D533.
38. Martusewitsch E, Sensen C, Schleper C (2000) High spontaneous mutation rate in the hyperthermophilic archaeaon Sulfolobus solfataricus is mediated by transposable elements. J Bacteriol 182: 2574-2581.
39. Masuda T, Tomita M, Ishihama Y (2008) Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res 7: 731-740.
40. Ni XY, Drengstig T, Ruoff P (2009) The control of the controller: molecular mechanisms for robust perfect adaptation and temperature compensation Biophys J (accepted).
41. Olivier BG, Snoep JL (2004) Web-based kinetic modelling using JWS Online. Bioinformatics 20: 2143-2144.
42. Pham TK, Sierocinski P, van der Oost J, Wright PC (2009) Quantitative proteomic analysis of Sulfolobus solfataricus membrane proteins. J Proteome Res (submitted).
43. Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32 Suppl: 496-501.
44. Redder P, She Q, Garrett RA (2001) Non-autonomous mobile elements in the Crenarchaeon Sulfolobus solfataricus. J Mol Biol 306: 1-6.
45. Ruggero D, Creti R, Londei P (1993) In vitro translation of archaeal natural mRNAs at high temperature. FEMS Microbiol Lett 107: 89-94.
46. Schleper C, Kubo K, Zillig W (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: 7645-7649.
47. Schleper C, Röder R, Singer T, Zillig W (1994) An insertion element of the extremely thermophilic archaeon Sulfolobus solfataricus transposes into the endogenous b-galactosidase gene. Mol Gen Genet 243: 91-96.
48. She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CCY, Groth Clausen I, Curtis B-A, De Moors A, Erauso G, Fletcher C, Gordon PMK, Heikamp-de Jong I, Jeffries AC, Kozera CJ, Medina N, Peng X, Thi-Ngoc HP, Redder P, Schenk ME, Theriault C, Tolstrup N, Charlebois RL, Doolittle WF, Duguet M, Gaasterland T, Garrett RA, Ragan MA, Sensen CW, van der Oost J (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. PNAS 98(14): 7835-7840.
49. Sherawat M, Tolan DR, Allen KN (2008) Structure of a rabbit muscle fructose-1, 6-bisphosphate aldolase A dimer variant. Acta Crystallogr D Biol Crystallogr 64(5): 543-550.
50. Skorko R, Osipiuk J, Stetter KO (1989) Glycogen-bound polyphosphate kinase from the archaebacterium Sulfolobus acidocaldarius. J Bacteriol 171: 5162-5164.
51. Snijders APL, Walther J, Peter S, Kinnman I, de Vos MGJ, van de Werken HJG, Brouns SJJ, van der Oost J, Wright PC (2006) Reconstruction of central carbon metabolism in Sulfolobus solafatricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis. Proteomics 6(15): 1518-1529.
52. Snoep JL, Westerhoff HV (2005) From isolation to integration, a systems biology approach for building the silicon cell. In: Westerhoff HV, Alberghina L (eds) Topics in current genetics (series): systems biology: definitions and perspectives, vol 13. Springer, Berlin, pp 13-30.
53. Strelkov S, von Elstermann M, Schomburg D (2004) Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography/mass spectrometry. Biol Chem 385: 853-861.
54. Studier FW, Moffat BA (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189: 113-130.
55. Tusher V, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98: 5116-5121.
56. van der Oost J, Siebers B (2007) The glycolytic pathways of Archaea: evolution by tinkering. In: Garrett RA, Klenk H-P (eds) Archaea: evolution, physiology and molecular biology, vol 22, pp 247-260. Blackwell, Malden.
57. Verhees CH, Kengen SW, Tuininga JE, Schut GJ, Adams MWW, De Vos WM, van der Oost J (2003) The unique features of glycolytic pathways in Archaea. Biochem J 375: 231-246 Erratum in: Biochem J (2004) 377: 819-822.
58. Verhees CH, Kengen SW, Tuininga JE, Schut GJ, Adams MWW, De Vos WM, van der Oost J (2004) The unique features of glycolytic pathways in Archaea. Biochem J 377: 819-822 (Erratum).
59. Wagner M, Berkner S, Ajon M, Driessen AJM, Lipps G, Albers SV (2009) Expanding and understanding the genetic toolbox of the hyperthermophilic genus Sulfolobus. Biochem Soc Trans 37: 97-101.
60. Weinberg MV, Schut GJ, Brehm S, Datta S, Adams MW (2005) Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins. J Bacteriol 187(1): 336-348.
61. Wernersson R, Nielsen HB (2005) OligoWiz 2. 0-integrating sequence feature annotation into design of microarray probes. Nucleic Acids Res 33: W611-W615.
62. Wessel D, Flugge UI (1984) A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal Biochem 138: 141-143.
63. Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA (2008) DBD-taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res 36 (database issue): D88-D92.
64. Worthington P, Hoang V, Perez-Pomares F, Blum P (2003) Targeted disruption of the alpha-amylase gene in the hyperthermophilic archaeon Sulfolobus solfataricus. J Bacteriol 185: 482-488.
65. Wu J, Wang S, Bai J, Shi L, Li D, Xu Z, Niu Y, Lu J, Bao Q (2008) ArchaeaTF: an integrated database of putative transcription factors in Archaea. Genomics 91(1): 102-107.
66. Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov W, Saeed AI, White J, Li J, Lee Yeatman TJ, Quackenbush J (2002) Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol 3: 0062. 1-0062. 12.
67. Zaparty M, Zaigler A, Stamme C, Soppa J, Hensel R, Siebers B (2008) DNA microarray analysis of the central carbohydrate metabolism: glycolytic/gluconeogenic carbon switch in the hyperthermophilic Crenarchaeum Thermoproteus tenax. J Bacteriol 190(6): 2231-2238.
68. Zillig W, Stetter KO, Wunderl S, Schulz W, Priess H, Scholz I (1980) The Sulfolobus-"Caldariella" Group: taxonomy on the basis of the structure of DNA-dependent RNA polymerases. Arch Microbiol 125: 259-269.
69. Zolghadr B, Weber S, Szabó Z, Driessen AJM, Albers SV (2007) Identification of a system required for the functional surface localization of sugar binding protein with class III signal peptides in Sulfolobus solfataricus. Mol Microbiol 64: 795-806.