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74.  Pedro-Loig, L., Lange, C., Bonete, MJ., Soppa, J., Maupin-Furlow, J. (2013) Nitrogen Regulation of protein-protein interactions and transcript levels of GlnK PII regulator and AmtB ammonium transporter homologs in Archaea. MicrobiologyOpen 2,826-840.

73.    Soppa, J. (2013) Evolutionary advantages of polyploidy in halophilic archaea. Biochem. Soc Trans 41, 339-343.

72. Heyer, R., Dörr, M., Jellen-Ritter, A., Späth, B., Babski, J., Jaschinski, K., Soppa, J., Marchfelder, A. (2012) High throughput sequencing reveals a plethora of small RNAs including tRNA derived fragments in Haloferax volcanii. RNA Biology 9 (7), 1011-1018.

71. Wurm, J.P., Griese, M., Bahr, U., Held, M., Heckel, A., Karas, M., Soppa, J., Wöhnert, J. (2012) Identification of the enzyme responsible for N1-methylation of pseudouridine 54 of archaeal tRNAs. RNA 18, 412-420.

70. Soppa, J.  (2011) Functional genomic and advanced genetic studies reveal novel insights into the metabolism, regulation, and biology of  Haloferax volcanii. Archaea 2011, Art. ID 602408, 14 pages.

69. Griese, M., Lange, C., Soppa, J.(2011) Ploidy in cyanobacteria. FEMS Microbiology Letters 323, 124-131.

68. Babski, J., Tjaden, B., Voss, B., Jellen-Ritter, A., Marchfelder, A., Hess, W., Soppa, J. (2011)Bioinformatic prediction and experimental verification of RNAs in the haloarchaeon Haloferax volcanii. RNA Biology 8 (5), 806-816.

67. Jantzer, K., Zerulla, K., Soppa, J. (2011) Phenotyping in the archaea: optimization of growth parameters and analysis of mutants of Haloferax volcanii.FEMS Microbiology Letters 322, 123-130.

66. Lange C., Zerulla K., Breuert S., Soppa, J.(2011) Gene conversion results in the equalization of genome copies in the polyploid Haloarchaeon Haloferax volcanii. Mol Microbiol 80 (3), 666-677.

65.Pecoraro, V., Zerulla, K., Lange, C., Soppa, J. (2011) Quantification of ploidy in proteobacteria revealed the existence of monoploid, (mero-) oligoploid and polyploid species.PLoS One6 (1) e16392.

64. Fischer, S., Benz, J., Spath, B., Jellen-Ritter, A., Heye,r R., Dorr, M., Maier, L.K., Menzel-Hobeck, C., Lehr, M.,Jantzer, K., Babski, J., Soppa, J., Marchfelder, A. (2011) Regulatory RNAs in Haloferax volcanii. Biochem. Soc Trans 39 (1): 159-162.

63. Soppa, J.(2011) Ploidy and gene conversion in Archaea. Biochem. Soc Trans 39 (1), 150-154.

62. Hildenbrand, C., Stock, T., Lange, C., Rother, M., Soppa, J. (2011) Genome copy numbers andgene conversion in methanogenic archaea. J Bacteriol 193 (3): 734-743.

61. Fischer, S., Benz, J., Spath, B., Maier, LK., Straub, J., Granzow, M., Raabe, M., Urlaub, H., Hoffmann, J., Brutschy, B., Allers, T., Soppa, J., Marchfelder, A. (2010) The archaeal Lsm protein binds to small RNAs. J Biol Chem. 285 (45), 34429-34438.

60. Eichler, J., Maupin-Furlow, J., Soppa, J. (2010) Archaeal protein biogenesis: posttranslational modification and degradation. Archaea 2010. Article ID 643046, 2 pages.

59. Soppa, J. (2010) Protein acetylation in archaea, bacteria, and eukaryotes. Archaea 2010. Article ID 820681, 9 pages.

58. Kopitz, A., Soppa, J., Hauser, K. (2010) Analysis of a hybrid TATA box binding protein originating from mesophilic and thermophilic donor organisms. Spectroscopy 24 (3-4), 233-237.

57.Sisignano, M., Morbitzer, D., Gatgens, J., Oldiges, M., Soppa, J. (2010) A 2-oxoacid dehydrogenase complex of Haloferax volcanii is essential for growth on isoleucine but not on other branched-chain amino acids. Microbiol 156 (2): 521-529.

56. Johnsen, U., Dambeck, M., Zaiß, H., Fuhrer, T., Soppa, J., Sauer, U., Schönheit, P. (2009) D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii. J Biol Chem 284: 27290-27303.

55. Kopitz, A., Soppa, J., Krejtschi, C., Hauser, K. (2009) Differential stability of TATA box binding proteins from archaea with different optimal growth temperatures. Spectrochimica Acta Part A: 73, 799-804.

54. Straub, J., Brenneis, M., Jellen-Ritter, A., Heyer, R., Soppa, J., Marchfelder, A. (2009) Small RNAs in haloarchaea: Identification, differential expression and biological function. RNA Biology 6(3).

53. Hering, O., Brenneis, M., Beer, J., Suess, B., Soppa, J. (2009) A novel mechanism for translation initiation operates in haloarchaea. Mol Microbiol 71, 1451-1463.

52. Brenneis, M., Soppa, J.(2009) Regulation of translation in haloarchaea: 5?- and 3?-UTRs are essential and have to functionally interact in vivo. PLOS One 4, e4484.

51. Soppa, J., Straub, J., Brenneis, M., Jellen-Ritter, A., Heyer, R., Fischer, S., Granzow, M., Voss, B., Hess, W., Tjaden, B., Marchfelder, A. (2009) Small RNAs of the halophilic archaeon Haloferax volcanii. Biochem Soc Trans 37, 133-136.

50. Huber, H, Soppa, J. (2008) Gene regulation and genome function in Archaea: a progress survey. Arch Microbiol 190, 195-196.

49. Pfeiffer, F., Schuster, S., Broicher, A., Falb, M., Palm, P., Rodeward, K., Ruepp, A., Soppa, J., Tittor, J., Oesterhelt, D. (2008) Genome sequences of Halobacterium salinarum: a reply. Genomics 91,553-554.

48. Hammelmann, M., Soppa, J. (2008) Optimized generation of vectors for the construction of Haloferax volcanii deletion mutants. J. Microbiol. Methods 75, 201-204.

47. Soppa, J., Baumann, A., Brenneis, M., Dambeck, M., Hering, O., Lange, C. (2008) Genomics and functional genomics with halophilic Archaea. Arch Microbiol 190, 197-215.

46. Dambeck, M., Soppa, J. (2008) Characterization of a Haloferax volcanii member of the enolase superfamily: deletion mutant construction, expression analysis, and transcriptome comparison. Arch Microbiol 190, 341-353.

45. Pfeiffer, F., Schuster, S., Broicher, A., Falb, M., Palm, P., Rodeward, K., Ruepp, A., Soppa, J., Tittor, J., and Oesterhelt, D. (2008) Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 as compared to strain NRC-1. Genomics 91, 335-346.

44. Zaparty, M., Zaigler, A., Stamme, C., Soppa, J., Hensel, R., and Siebers, B. (2008) DNA microarray analysis of the central carbohydrate metabolism: glycolytic / gluconeogenetic carbon switch in the hyperthermophilic crenarchaeum of Thermoproteus tenax. J. Bacteriol 190, 2231-2238.

43. Lange, C., Zaigler, A., Hammelmann, M., Twellmeyer, J., Raddatz, G., Schuster, S., Oesterhelt, D., and Soppa, J. (2007) Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea. BMC Genomics 8, 415.

42. Brenneis, M., Hering, O., Lange, C., and Soppa, J. (2007) Experimental characterization of cis-acting elements important for translation and transcription in halophilic Archaea. PLoS Genet 3(12): e229.

41. Large, A., Stamme, C., Lange, C., Duan, Z., Allers, T., Soppa, J., and Lund, P. A. (2007) Characterization of a tightly controlled promoter of the halophilic archaeon Haloferax volcanii and its use in the analysis of the essential cct1 gene. Mol Microbiol66(5), 1092-1106.

40. Twellmeyer, J., Wende, A., Wolfertz, J., Pfeiffer, F., Panhuysen, M., Zaigler, A., Soppa, J., Welzl, G., and Oesterhelt, D. (2007) Microarray Analysis in the Archaeon Halobacterium salinarum Strain R1. PLoS ONE 2, e1064.

39. Hundt, S., Zaigler, A., Lange, C., Soppa, J., and Klug, G. (2007) Global analysis of mRNA decay in Halobacterium salinarum NRC-1 at single-gene resolution using DNA microarrays. J Bacteriol 189, 6936-6944.

38. van Ooyen, J., and Soppa, J. (2007) Three 2-oxoacid dehydrogenase operons in Haloferax volcanii: expression, deletion mutants and evolution. Microbiology 153, 3303-3313.

37. Baumann, A., Lange, C. and Soppa, J. (2007) Transcriptome changes and cAMP oscillations in an archaeal cell cycle. BMC Cell Biol. 8:21.

36. Breuert, S., Allers, T., Spohn, G. and Soppa, J. (2006) Regulated polyploidy in halophilic archaea. PLoS ONE, 1, e92.

35. Soppa, J. (2006) From genomes to function: haloarchaea as model organisms. Microbiology, 152, 585-590.

34. Soppa, J. (2005) From replication to cultivation: hot news from Haloarchaea. Curr Opin Microbiol, 8, 737-744.

33. Zaigler, A., Schuster, S.C. and 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.

32. Herrmann, U. and Soppa, J. (2002) Cell cycle-dependent expression of an essential SMC-like protein and dynamic chromosome localization in the archaeon Halobacterium salinarum. Mol Microbiol, 46, 395-409.

31. Soppa, J., Kobayashi, K., Noirot-Gros, M.F., Oesterhelt, D., Ehrlich, S.D., Dervyn, E., Ogasawara, N. and Moriya, S. (2002) Discovery of two novel families of proteins that are proposed to interact with prokaryotic SMC proteins, and characterization of the Bacillus subtilis family members ScpA and ScpB. Mol Microbiol, 45, 59-71.

30. Mascarenhas, J., Soppa, J., Strunnikov, A.V. and Graumann, P.L. (2002) Cell cycle-dependent localization of two novel prokaryotic chromosome segregation and condensation proteins in Bacillus subtilis that interact with SMC protein. EMBO J, 21, 3108-3118.

29. Wanner, C. and Soppa, J. (2002) Functional role for a 2-oxo acid dehydrogenase in the halophilic archaeon Haloferax volcanii. J Bacteriol, 184, 3114-3121.

28. Soppa, J. (2001) Basal and regulated transcription in archaea. Adv Appl Microbiol, 50, 171-217.

27. Soppa, J. (2001) Prokaryotic structural maintenance of chromosomes (SMC) proteins: distribution, phylogeny, and comparison with MukBs and additional prokaryotic and eukaryotic coiled-coil proteins. Gene, 278, 253-264.

26. Wanner, C. and Soppa, J. (1999) Genetic identification of three ABC transporters as essential elements for nitrate respiration in Haloferax volcanii. Genetics, 152, 1417-1428.

25. Soppa, J. (1999) Transcription initiation in Archaea: facts, factors and future aspects. Mol Microbiol, 31, 1295-1305.

24. Soppa, J. (1999) Normalized nucleotide frequencies allow the definition of archaeal promoter elements for different archaeal groups and reveal base-specific TFB contacts upstream of the TATA box. Mol Microbiol, 31, 1589-1592.

23. Patenge, N. and Soppa, J. (1999) Extensive proteolysis inhibits high-level production of eukaryal G protein-coupled receptors in the archaeon Haloferax volcanii. FEMS Microbiol Lett, 171, 27-35.

22. Soppa, J., Vatter, P., Ruepp, A., Zur Mühlen, A. and Link, T.A. (1998) Regulation of gene expression in Halobacterium salinarum: The arcRACB gene cluster and the TATA box-binding protein. Microbiology and Biogeochemistry of Hypersaline Environments. Edited by Aharon Oren.CRC press, 249-263.

21. Soppa, J. (1998) Optimization of the 5-bromo-2 '-deoxyuridine selection and its application for the isolation of nitrate respiration-deficient mutants of Haloferax volcanii. J Microbiol Meth, 34, 41-48.

20. Ruepp, A., Wanner, G. and Soppa, J. (1998) A 71-kDa protein from Halobacterium salinarium belongs to a ubiquitous P-loop ATPase superfamily with head-rod-tail structure. Arch Microbiol, 169, 1-9.

19. Soppa, J. and 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.

18. Sohlemann, P., Soppa, J., Oesterhelt, D. and Lohse, M.J. (1997) Expression of beta 2-adrenoceptors in halobacteria. Naunyn Schmiedebergs Arch Pharmacol, 355, 150-160.

17. Ruepp, A. and Soppa, J. (1996) Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster. J Bacteriol, 178, 4942-4947.

16. Danner, S. and Soppa, J. (1996) Characterization of the distal promoter element of halobacteria in vivo using saturation mutagenesis and selection. Mol Microbiol, 19, 1265-1276.

15. Ruepp, A., Muller, H.N., Lottspeich, F. and Soppa, J. (1995) Catabolic ornithine transcarbamylase of Halobacterium halobium (salinarium): purification, characterization, sequence determination, and evolution. J Bacteriol, 177, 1129-1136.

14. Soppa, J. (1994) Compilation of halobacterial protein-coding genes, the halobacterial codon usage table and its use. Syst Appl Microbiol, 16, 725-733.

13. Soppa, J. (1994) Sequence comparison doesnot support an evolutionary link between halobacterial retinal proteins including bacteriorhodopsin and eukariotic G-protein-coupled receptors. FEBS Lett, 342, 7-11.

12. Soppa, J., Duschl, J. and Oesterhelt, D. (1993) Bacterioopsin, haloopsin, and sensory opsin I of the halobacterial isolate Halobacterium sp. strain SG1: three new members of a growing family. J Bacteriol, 175, 2720-2726.

11. Govindjee, R., Kono, M., Lukashev, E., Balashov, S., Ebrey, T., Soppa, J., Tittor, J. and Oesterhelt, D. (1993) Spectral and photochemical properties of Y57N mutant of bacteriorhodopsin. Biophys. J., 64, A212.

10. Govindjee, R., Lukashev, E., Kono, M., Balashov, S., Ebrey, T., Soppa, J., Tittor, J. and Oesterhelt, D. (1992) Tyr57Asn mutant of bacteriorhodopsin: M formation and spectral transformations at high pH. Structure and fuctions of retinal proteins. Colloque INSERM, J. L. E. Ltd. Montrouge. 221, 115-118.

09. Engelhard, M., Hess, B., Metz, G., Kreutz, W., Siebert, F., Soppa, J. and Oesterhelt, D. (1990) High resolution 13C-solid state NMR of bacteriorhodopsin: assignment of specific aspartic acids and structural implications of single site mutations. Eur Biophys J, 18, 17-24.

08. Gerwert, K., Hess, B., Soppa, J. and Oesterhelt, D. (1989) Role of aspartate-96 in proton translocation by bacteriorhodopsin. Proc Natl Acad Sci U S A, 86, 4943-4947.

07. Soppa, J., Otomo, J., Straub, J., Tittor, J., Meessen, S. and Oesterhelt, D. (1989) Bacteriorhodopsin mutants of Halobacterium sp. GRB. II. Characterization of mutants. J Biol Chem, 264, 13049-13056

06. Soppa, J. and Oesterhelt, D. (1989) Bacteriorhodopsin mutants of Halobacterium sp. GRB. I. The 5-bromo-2'-deoxyuridine selection as a method to isolate point mutants in halobacteria. J Biol Chem, 264, 13043-13048.

05. Soppa, J. and Oesterhelt, D. (1989) Halobacterium sp. GRB: a species to work with! Can J Microbiol, 35, 205-209.

04. Overath, P., Weigel, U., Neuhaus, J.M., Soppa, J., Seckler, R., Riede, I., Bocklage, H., Muller-Hill, B., Aichele, G. and Wright, J.K. (1987) Lactose permease of Escherichia coli: properties of mutants defective in substrate translocation. Proc Natl Acad Sci U S A, 84, 5535-5539.

03. Soppa, J., Seckler, R., Wright, J., Weigel, U., Neuhaus, J. and Overath, P. (1985) Genetic-evidence for binding and translocation as separate steps in lactose carrier function. Biol Chem, 366, 855.

02. Neuhaus, J.M., Soppa, J., Wright, J.K., Riede, I., Blocker, H., Frank, R. and Overath, P. (1985) Properties of a mutant lactose carrier of Escherichia coli with a Cys148----Ser148 substitution. FEBS Lett, 185, 83-88.

01. Klump, W., Soppa, J., Marquardt, O. and Hofschneider, P. (1984), Expression of the foot and mouth disease virus protease in E.Coli. 35. Colloquium Mosbach. Springer Verlag, pp. 201-209.

 

 

 

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