Publications
List of publications (with peer review)
Updated: March 2022
111. Soppa J. (2022) Non-equivalent genomes in polyploid prokaryotes.
110. Schramm F., Borst A., Linne U., Soppa J. (2021) Elucidation of the translation initiation factor network of Haloferax volcanii reveals coupling of transcription and translation in haloarchaea.
109. Fuchino K, Wasser D., Soppa J. (2021) Genome copy number quantification revealed that the ethanologenic alpha-proterbacterium Zymomonas mobilis is polyploid.
108. Wasser D., Borst A., Hammelmann M., Ludt K., Soppa J. (2021) Characterization of non-selected intermolecular gene conversion in the polyploid haloarchaeaon Haloferax volcanii.
107. Zahn S, Kubatova N, Pyper DJ, Cassidy L, Saxena K, Tholey A, Schwalbe H, Soppa J. (2021). Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii.
106. Niessen, N., Soppa, J. (2020) Regulated iron siderophore production of the halophilic archaeon Haloferax volcanii.
105. Wolters, M., Borst, A., Pfeiffer, F., Soppa, J. (2020). Bioinformatic and genetic characterization of three genes localized adjacent tot he major replication origin of Haloferax volcanii.
104. Kubatova, N., Pyper, D.J., Jonker, H.R.A., Saxena, K., Remmel, L., Richter ,C., Brantl, S., Evguenieva-Hackenberg, E., Hess, W.R., Klug, G., Marchfelder, A., Soppa, J., Streit, W., Mayzel, M., Orekhov, V.Y., Fuxreiter, M., Schmitz, R.A., Schwalbe, H. (2020). Rapid biophysical characterization and NMR spectroscopy structural analysis of small proteins from bacteria and archaea.
103. Huber, M., Faure, G., Laass, S., Kolbe, E., Seitz, K., Wehrheim, C., Wolf, Y.I., Koonin, E.V., Soppa, J. (2019) Translational coupling via termination-reinitiation in archaea and bacteria.
102. Ludt, K., Soppa, J. (2019) Polyploidy in halophilic Archaea: Regulation, evolutionary advantages, and gene conversion.
101. Kliemt, J., Jaschinski, K., Soppa, J. (2019) A haloarchaeal small regulatory RNA (sRNA) is essential for rapid adaptation to phosphate starvation conditions.
100. Nagel, C., Machulla, A., Zahn, S., Soppa, J. (2019) Several one-domain zinc finger 碌-proteins of Haloferax volcanii are important for stress adaptation, biofilm formation, and swarming.
99. Laass, S., Monzon, V.A., Kliemt, J., Hammelmann, M., Pfeiffer, F., F枚rstner, K.U., Soppa, J. (2019) Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq.
98. Ludt, K., Soppa, J. (2018) Influence of origin recognition complex proteins on the copy numbers of three chromosomes in Haloferax volcanii.
97. Ludwig, P., Huber, M., Lehr, M., Wegener, M., Zerulla, K., Lange, C., Soppa, J. (2018) Non-canonical Escherichia coli transcripts lacking a Shine-Dalgarno motif have very different translational efficiencies and do not form a coherent group. doi: .
96. B枚ttinger, B., Semmler, F., Zerulla, K., Ludt, K., Soppa, J. (2018) Regulated ploidy of Bacillus subtilis and three new isolates of Bacillus and Paenibacillus. , doi: 10.1093/femsle/fnx282.
95. Kliemt, J, Soppa, J. (2017) Diverse functions of small RNAs (sRNAs) in halophilic Archaea: From non-coding regulatory RNAs to microprotein-encoding sRNAs. In:
94. Maurer, S., Ludt, K, Soppa, J. (2017) Characterization of copy number control of two Haloferax volcanii replication origins using deletion mutants and Haloarchaeal Artificial Chromosomes.
93. Soppa, J. (2017) Polyploidy and community struchture.
92. Lange, C., Lehr, M., Zerulla, K., Ludwig, P., Schweitzer, J., Polen, T., Wendisch, VF. and Soppa, J. (2017) Effects of Kasugamycin on the Translatome of Escherichia coli.
91. Wegener, M., Vogtmann, K., Huber, M., Laa脽, S. and Soppa, J. (2016) The glpD gene is a novel reporter gene for E. coli that is superior to established reporter genes like lacZ and gusA.
90. Babski, J., Haas, KA., N盲ther-Schindler, D., Pfeiffer, F., F枚rstner, KU. et al. (2016) Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq).
89. Sutter, J.M., Tastensen, J.B., Johnsen, U., Soppa, J. and Schonheit, P. (2016) Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase.
88. Zerulla, K., Ludt, K. and Soppa, J. (2016) The ploidy level of Synechocystis sp. PCC6803 is highly variable and is influenced by growth phase and by chemical and physical external parameters.
87. Maier, L. K., Benz, J., Fischer, S., Alstetter, M., Jaschinski, K., Hilker, R., Becker, A., Allers, T., Soppa, J. and Marchfelder, A. (2015). Deletion of the Sm1 encoding motif in the lsm gene results in distinct changes in the transcriptome and enhanced swarming activity of Haloferax cells. .
86. Soppa, J. (2014). Polyploidy in Archaea and Bacteria: About desiccation resistance, giant cell size, long-term survival, enforcement by a eukaryotic host and additional aspects. J. .
85. Jaakkola, ST., Zerulla, K., Guo, Q., Liu, Y., Ma, H., Yang, C., Bamford, DH., Chen, X., Soppa, J. and Oksanen, HM. (2014) Halophilic archaea cultivated from surface sterilized middle-late eocene rock salt are polyploidy. .
84. Zerulla, K., Baumann, A. and Soppa, J. (2014). Cell Cycle and Polyploidy in Haloarchaea. In: Genetics and Genomics of Halophiles, eds. R.T. Papke and A. Oren (Horizon Scientific Press) 146-166.
83. Zerulla, K., Soppa, J. (2014) Polyploidy in haloarchaea: advantages for growth and survival.
82. Babski, J., Maier, L-K., Heyer, R., Jaschinski, K., Prasse, D., J盲ger, D., Randau, L., Schmitz, RA., Marchfelder, A., Soppa, J. (2014) Small regulatory RNAs in Archaea.
81. Kramer, P., G盲bel, K., Pfeiffer, F., Soppa, J. (2014) Haloferax volcanii, a prokaryotic species that does not use the Shine Dalgarno mechanism for translation initiation at 5'-UTRs.
80. Zerulla, K., Chimileski, S., N盲ther, D., Gophna, U., Papke, RT., Soppa, J. (2014) DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival.
79. Jaschinski, K., Babski, J., Lehr, M., Burmester, A., Benz, J., Heyer, R., D枚rr, M., Marchfelder, A., Soppa, J. (2014) Generation and phenotyping of a collection of sRNA gene deletion mutants of the haloarchaeon Haloferax volcanii.
78. G盲bel, K., Schmitt, J., Schulz, S., N盲ther, D., Soppa, J. (2013) A comprehensive analysis of the importance of translation initiation factors for Haloferax volcanii applying deletion and conditional depletion mutants.
77. 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.
Soppa, J. (2013) Evolutionary advantages of polyploidy in
halophilic archaea.
76. Heyer, R., D枚rr, M., Jellen-Ritter, A., Sp盲th, 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.
75. Wurm, J.P., Griese, M., Bahr, U., Held, M., Heckel, A., Karas, M., Soppa, J., W枚hnert, J. (2012) Identification of the enzyme responsible for N1-methylation of pseudouridine 54 of archaeal tRNAs.
74. Soppa, J. (2011) Functional genomic and advanced genetic studies reveal novel insights into the metabolism, regulation, and biology of Haloferax volcanii.
73. Griese, M., Lange, C., Soppa, J.(2011) Ploidy in cyanobacteria.
72. 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.
71. Jantzer, K., Zerulla, K., Soppa, J. (2011) Phenotyping in the archaea: optimization of growth parameters and analysis of mutants of Haloferax volcanii.
70. Lange C., Zerulla K., Breuert S., Soppa, J.(2011) Gene conversion results in the equalization of genome copies in the polyploid Haloarchaeon Haloferax volcanii.
69. Pecoraro, V., Zerulla, K., Lange, C., Soppa, J. (2011) Quantification of ploidy in proteobacteria revealed the existence of monoploid, (mero-) oligoploid and polyploid species.
68. 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.
67. Soppa, J. (2011) Initiation and regulation of translation in halophilic archaea. In: Halophiles and hypersaline environments. Ventosa, A., Oren A., Ma, Y.H. (edt.) Springer Berlin, p. 191-205.
66. Soppa, J.(2011) Ploidy and gene conversion in Archaea.
65. Hildenbrand, C., Stock, T., Lange, C., Rother, M., Soppa, J. (2011) Genome copy numbers andgene conversion in methanogenic archaea.
64. Schmitz-Streit, R., J盲ger, D., Jellen-Ritter, A., Babski, J., Soppa, J., Marchfelder, A. (2011) Archaea employ small RNAs as regulators. In: Regulatory RNAs in prokaryotes. Hess, W.R., Marchfelder, A. (edt.) Springer Berlin, p. 131-145.
63. Soppa, J. (2011) Initiation and regulation of translation in halophilic archaea. In: Halophiles and hypersaline environments. Ventosa, A., Oren A., Ma, Y.H. (edt.) Springer Berlin, p. 191-205.
62. 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.
61. Eichler, J., Maupin-Furlow, J., Soppa, J. (2010) Archaeal protein biogenesis: posttranslational modification and degradation. Archaea 2010.
60. Soppa, J. (2010) Protein acetylation in archaea, bacteria, and eukaryotes.Archaea 2010.
59. Kopitz, A., Soppa, J., Hauser, K. (2010) Analysis of a hybrid TATA box binding protein originating from mesophilic and thermophilic donor organisms.
58. 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. .
57. Johnsen, U., Dambeck, M., Zai脽, H., Fuhrer, T., Soppa, J., Sauer, U., Sch枚nheit, P. (2009) D-xylose degradation pathway in the halophilic archaeonHaloferax volcanii.
56. Kopitz, A., Soppa, J., Krejtschi, C., Hauser, K. (2009) Differential stability of TATA box binding proteins from archaea with different optimal growth temperatures.
55. Straub, J., Brenneis, M., Jellen-Ritter, A., Heyer, R., Soppa, J., Marchfelder, A. (2009) Small RNAs in haloarchaea: Identification, differential expression and biological function.
54. Hering, O., Brenneis, M., Beer, J., Suess, B., Soppa, J. (2009) A novel mechanism for translation initiation operates in haloarchaea.
53. Brenneis, M., Soppa, J.(2009) Regulation of translation in haloarchaea: 5?- and 3?-UTRs are essential and have to functionally interact in vivo.
52. 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.
51. Huber, H, Soppa, J. (2008) Gene regulation and genome function in Archaea: a progress survey.
50. Pfeiffer, F., Schuster, S., Broicher, A., Falb, M., Palm, P., Rodeward, K., Ruepp, A., Soppa, J., Tittor, J., Oesterhelt, D. (2008) Genome sequences ofHalobacterium salinarum: a reply.
49. Hammelmann, M., Soppa, J. (2008) Optimized generation of vectors for the construction of Haloferax volcanii deletion mutants. J. Microbiol. Methods75, 201-204.
48. 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.
47. Dambeck, M., Soppa, J. (2008) Characterization of a Haloferax volcaniimember of the enolase superfamily: deletion mutant construction, expression analysis, and transcriptome comparison.
46. 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.
45. 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.
44. 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.
43. Brenneis, M., Hering, O., Lange, C., and Soppa, J. (2007) Experimental characterization of cis-acting elements important for translation and transcription in halophilic Archaea.
42. 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.
41. 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.
40. 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.
39. van Ooyen, J., and Soppa, J. (2007) Three 2-oxoacid dehydrogenase operons in Haloferax volcanii: expression, deletion mutants and evolution.
38. Baumann, A., Lange, C. and Soppa, J. (2007) Transcriptome changes and cAMP oscillations in an archaeal cell cycle.
37. Breuert, S., Allers, T., Spohn, G. and Soppa, J. (2006) Regulated polyploidy in halophilic archaea.
36. Soppa, J. (2006) From genomes to function: haloarchaea as model organisms.
35. Soppa, J. (2005) From replication to cultivation: hot news from Haloarchaea.
34. 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.
33. 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.
32. 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.
31. 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.
30. Wanner, C. and Soppa, J. (2002) Functional role for a 2-oxo acid dehydrogenase in the halophilic archaeon Haloferax volcanii.
29. Soppa, J. (2001) Basal and regulated transcription in archaea.
28. Soppa, J. (2001) Prokaryotic structural maintenance of chromosomes (SMC) proteins: distribution, phylogeny, and comparison with MukBs and additional prokaryotic and eukaryotic coiled-coil proteins.
27. Wanner, C. and Soppa, J. (1999) Genetic identification of three ABC transporters as essential elements for nitrate respiration in Haloferax volcanii.
26. Soppa, J. (1999) Transcription initiation in Archaea: facts, factors and future aspects.
25. 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.
24. Patenge, N. and Soppa, J. (1999) Extensive proteolysis inhibits high-level production of eukaryal G protein-coupled receptors in the archaeon Haloferax volcanii.
23. Soppa, J., Vatter, P., Ruepp, A., Zur M眉hlen, 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.
22. Soppa, J. (1998) Optimization of the 5-bromo-2 '-deoxyuridine selection and its application for the isolation of nitrate respiration-deficient mutants ofHaloferax volcanii. J Microbiol Meth, 34, 41-48.
21. Ruepp, A., Wanner, G. and Soppa, J. (1998) A 71-kDa protein fromHalobacterium salinarium belongs to a ubiquitous P-loop ATPase superfamily with head-rod-tail structure.
20. Soppa, J. and Link, T.A. (1997) The TATA-box-binding protein (TBP) ofHalobacterium salinarum. Cloning of the tbp gene, heterologous production of TBP and folding of TBP into a native conformation.
19. Sohlemann, P., Soppa, J., Oesterhelt, D. and Lohse, M.J. (1997) Expression of beta 2-adrenoceptors in halobacteria.
18. Ruepp, A. and Soppa, J. (1996) Fermentative arginine degradation inHalobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster.
17. Danner, S. and Soppa, J. (1996) Characterization of the distal promoter element of halobacteria in vivo using saturation mutagenesis and selection.
16. Ruepp, A., Muller, H.N., Lottspeich, F. and Soppa, J. (1995) Catabolic ornithine transcarbamylase of Halobacterium halobium (salinarium): purification, characterization, sequence determination, and evolution.
15. Soppa, J. (1994) Compilation of halobacterial protein-coding genes, the halobacterial codon usage table and its use. Syst Appl Microbiol, 16, 725-733.
14. Soppa, J. (1994) Sequence comparison doesnot support an evolutionary link between halobacterial retinal proteins including bacteriorhodopsin and eukariotic G-protein-coupled receptors.
13. 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.
12. 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.
11. 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.
10. 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.
9. Gerwert, K., Hess, B., Soppa, J. and Oesterhelt, D. (1989) Role of aspartate-96 in proton translocation by bacteriorhodopsin.
8. Soppa, J., Otomo, J., Straub, J., Tittor, J., Meessen, S. and Oesterhelt, D. (1989) Bacteriorhodopsin mutants of Halobacterium sp. GRB. II. Characterization of mutants.
7. Soppa, J. and Oesterhelt, D. (1989) Bacteriorhodopsin mutants ofHalobacterium sp. GRB. I. The 5-bromo-2'-deoxyuridine selection as a method to isolate point mutants in halobacteria.
6. Soppa, J., Oesterhelt, D. (1987) Isolation and characterization of bacteriorhodopsin mutants of Halobacterium spec. GRB. Biol Chem, 368, 1116.
5. Soppa, J. and Oesterhelt, D. (1989) Halobacterium sp. GRB: a species to work with!
4. 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.
3. 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.
2. 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 coliwith a Cys148----Ser148 substitution.
1. 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.