From genomes to function: haloarchaea as model organisms

References

1. Allers T, Ngo H. P, Mevarech M, Lloyd R. G. 2004; Development of additional selectable markers for the halophilic archaeon Haloferax volcanii based on the leuB and trpA genes. Appl Environ Microbiol 70:943–953 [CrossRef]
   [Google Scholar]
2. Baliga N. S, Pan M, Goo Y. A. 7 other authors 2002; Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A 99:14913–14918 [CrossRef]
   [Google Scholar]
3. Baliga N. S, Bjork S. J, Bonneau R, Pan M, Iloanusi C, Kottemann M. C, Hood L, DiRuggiero J. 2004a; Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res 14:1025–1035 [CrossRef]
   [Google Scholar]
4. Baliga N. S, Bonneau R, Facciotti M. T. 12 other authors 2004b; Genome sequence of Haloarcula marismortui : a halophilic archaeon from the Dead Sea. Genome Res 14:2221–2234 [CrossRef]
   [Google Scholar]
5. Berquist B. R, DasSarma S. 2003; An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J Bacteriol 185:5959–5966 [CrossRef]
   [Google Scholar]
6. Bidle K. A. 2003; Differential expression of genes influenced by changing salinity using RNA arbitrarily primed PCR in the archaeal halophile Haloferax volcanii . Extremophiles 7:1–7
   [Google Scholar]
7. Bitan-Banin G, Ortenberg R, Mevarech M. 2003; Development of a gene knockout system for the halophilic archaeon Haloferax volcanii by use of the pyrE gene. J Bacteriol 185:772–778 [CrossRef]
   [Google Scholar]
8. Bonneau R, Baliga N. S, Deutsch E. W, Shannon P, Hood L. 2004; Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol 5:R52 [CrossRef]
   [Google Scholar]
9. Choi J, Joo W. A, Park S. J, Lee S. H, Kim C. W. 2005; An efficient proteomics based strategy for the functional characterization of a novel halophilic enzyme from Halobacterium salinarum . Proteomics 5:907–917 [CrossRef]
   [Google Scholar]
10. Ebel C, Costenaro L, Pascu M, Faou P, Kernel B, Proust-De Martin F, Zaccai G. 2002; Solvent interactions of halophilic malate dehydrogenase. Biochemistry 41:13234–13244 [CrossRef]
    [Google Scholar]
11. Goo Y. A, Roach J, Glusman G. 7 other authors 2004; Low-pass sequencing for microbial comparative genomics. BMC Genomics 5:3 [CrossRef]
    [Google Scholar]
12. Gordeliy V. I, Labahn J, Moukhametzianov R. 8 other authors 2002; Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex. Nature 419:484–487 [CrossRef]
    [Google Scholar]
13. Gregor D, Pfeifer F. 2005; In vivo analyses of constitutive and regulated promoters in halophilic archaea. Microbiology 151:25–33 [CrossRef]
    [Google Scholar]
14. Irihimovitch V, Ring G, Elkayam T, Konrad Z, Eichler J. 2003; Isolation of fusion proteins containing SecY and SecE, components of the protein translocation complex from the halophilic archaeon Haloferax volcanii . Extremophiles 7:71–77
    [Google Scholar]
15. Jäger A, Samorski R, Pfeifer F, Klug G. 2002; Individual gvp transcript segments in Haloferax mediterranei exhibit varying half-lives, which are differentially affected by salt concentration and growth phase. Nucleic Acids Res 30:5436–5443 [CrossRef]
    [Google Scholar]
16. Karadzic I. M, Maupin-Furlow J. A. 2005; Improvement of two-dimensional gel electrophoresis proteome maps of the haloarchaeon Haloferax volcanii . Proteomics 5:354–359 [CrossRef]
    [Google Scholar]
17. Klein C, Garcia-Rizo C, Bisle B, Scheffer B, Zischka H, Pfeiffer F, Siedler F, Oesterhelt D. 2005; The membrane proteome of Halobacterium salinarum . Proteomics 5:180–197 [CrossRef]
    [Google Scholar]
18. Levin I, Giladi M, Altman-Price N, Ortenberg R, Mevarech M. 2004; An alternative pathway for reduced folate biosynthesis in bacteria and halophilic archaea. Mol Microbiol 54:1307–1318 [CrossRef]
    [Google Scholar]
19. Lopalco P, Lobasso S, Babudri F, Corcelli A. 2004; Osmotic shock stimulates de novo synthesis of two cardiolipins in an extreme halophilic archaeon. J Lipid Res 45:194–201
    [Google Scholar]
20. Lundgren M, Andersson A, Chen L, Nilsson P, Bernander R. 2004; Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination. Proc Natl Acad Sci U S A 101:7046–7051 [CrossRef]
    [Google Scholar]
21. Marg B. L, Schweimer K, Sticht H, Oesterhelt D. 2005; A two-alpha-helix extra domain mediates the halophilic character of a plant-type ferredoxin from halophilic archaea. Biochemistry 44:29–39 [CrossRef]
    [Google Scholar]
22. McCready S, Müller J. A, Boubriak I, Berquist B. R, Ng W. L, DasSarma S. 2005; UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp . NRC-I. Saline Systems 1:3 [CrossRef]
    [Google Scholar]
23. Müller J. A, DasSarma S. 2005; Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N -oxide as terminal electron acceptors. J Bacteriol 187:1659–1667 [CrossRef]
    [Google Scholar]
24. Ng W. V, Kennedy S. P, Mahairas G. G. 40 other authors 2000; Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A 97:12176–12181 [CrossRef]
    [Google Scholar]
25. Peck R. F, DasSarma S, Krebs M. P. 2000; Homologous gene knockout in the archaeon Halobacterium salinarum with ura3 as a couterselectable marker. Mol Microbiol 35:667–676
    [Google Scholar]
26. Reuter C. J, Maupin-Furlow J. A. 2004; Analysis of proteasome-dependent proteolysis in Haloferax volcanii cells, using short-lived green fluorescent proteins. Appl Environ Microbiol 70:7530–7538 [CrossRef]
    [Google Scholar]
27. Sartorius-Neef S, Pfeifer F. 2004; In vivo studies on putative Shine-Dalgarno sequences of the halophilic archaeon Halobacterium salinarum . Mol Microbiol 51:579–588 [CrossRef]
    [Google Scholar]
28. Schobert B, Brown L. S, Lanyi J. K. 2003; Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base. J Mol Biol 330:553–570 [CrossRef]
    [Google Scholar]
29. Shmuely H, Dinitz E, Dahan I, Eichler J, Fischer D, Shaanan B. 2004; Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins. Bioinformatics 20:1248–1253 [CrossRef]
    [Google Scholar]
30. Soppa J. 2005; From replication to cultivation: hot news from haloarchaea. Curr Opin Microbiol 8:737–744 [CrossRef]
    [Google Scholar]
31. Soppa J, Link T. A. 1997; The TATA-box-binding protein (TBP) of Halobacterium salinarum . Cloning of the tbp gene, heterologous production of TBP and folding of TBP into a native conformation. Eur J Biochem 249:318–324 [CrossRef]
    [Google Scholar]
32. Tebbe A, Klein C, Bisle B. & 7 other authors; 2005; Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation. Proteomics 5:168–179 [CrossRef]
    [Google Scholar]
33. Tu D, Blaha G, Moore P. B, Steitz T. A. 2005; Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Cell 121:257–270 [CrossRef]
    [Google Scholar]
34. Wang G, Kennedy S. P, Fasiludeen S, Rensing C, DasSarma S. 2004; Arsenic resistance in Halobacterium sp. strain NRC-1 examined by using an improved gene knockout system. J Bacteriol 186:3187–3194 [CrossRef]
    [Google Scholar]
35. Wanner C, Soppa J. 1999; Genetic identification of three ABC transporters as essential elements for nitrate respiration in Haloferax volcanii . Genetics 152:1417–1428
    [Google Scholar]
36. Wanner C, Soppa J. 2002; Functional role for a 2-oxo acid dehydrogenase in the halophilic archaeon Haloferax volcanii . J Bacteriol 184:3114–3121 [CrossRef]
    [Google Scholar]
37. Wright D. B, Banks D. D, Lohman J. R, Hilsenbeck J. L, Gloss L. M. 2002; The effect of salts on the activity and stability of Escherichia coli and Haloferax volcanii dihydrofolate reductases. J Mol Biol 323:327–344 [CrossRef]
    [Google Scholar]
38. Zaigler A, Schuster S. C, Soppa J. 2003; Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii . Mol Microbiol 48:1089–1105 [CrossRef]
    [Google Scholar]
39. Zeth K, Offermann S, Essen L. O, Oesterhelt D. 2004; Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states. Proc Natl Acad Sci U S A 101:13780–13785 [CrossRef]
    [Google Scholar]
40. Zhang R, Zhang C. T. 2003; Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem Biophys Res Commun 302:728–734 [CrossRef]
    [Google Scholar]
41. Zhang R, Zhang C. T. 2005; Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea 1:335–346 [CrossRef]
    [Google Scholar]
42. Zimmermann P, Pfeifer F. 2003; Regulation of the expression of gas vesicle genes in Haloferax mediterranei : interaction of the two regulatory proteins GvpD and GvpE. Mol Microbiol 49:783–794
    [Google Scholar]