Archives of Microbiology

, Volume 190, Issue 3, pp 309–318 | Cite as

Variations in the multiple tbp genes in different Halobacterium salinarum strains and their expression during growth

  • Katharina Teufel
  • Anne Bleiholder
  • Tim Griesbach
  • Felicitas PfeiferEmail author
Original Paper


The presence and expression of the multiple tbp genes encoding TATA-box binding proteins (TBPs) was investigated in various strains and mutants of the archaeon Halobacterium salinarum. Six genes, tbpA through tbpF, are present in the genome of Hbt. salinarum NRC-1 and also in the gas vesicle negative mutant strain R1. The only tbp gene located in the chromosome is tbpE, whereas all others are found in the plasmid DNA. Due to the dynamic nature of the plasmids in the Halobacterium strains, the copy numbers of the alternative tbp genes vary significantly. Five tbp genes (tbpA through tbpE) were present in the wild-type strain Hbt. salinarum PHH1. The tbpC gene of Hbt. salinarum PHH1 carried an ISH27-2 insertion element at the start of the reading frame that prevented the expression. All other tbp genes of PHH1 were expressed under aerobic and anaerobic growth conditions and quantitative RT-PCR yielded tbpE as dominant tbp transcript during the exponential growth phase. The plasmid deletion variant Hbt. salinarum PHH4 lacked all of the tbp genes except for tbpE and showed an altered growth behaviour compared to PHH1 wild-type in the stationary growth phase under anaerobic growth conditions.


TBP proteins Plasmid variation ISH elements Alternative tbp genes 



TATA-box binding protein


RNA polymerase


Transcription factor B


Quantitative reverse transcriptase polymerase chain reaction



We thank Arnulf Kletzin for valuable discussions and Simone Sartorius-Neef, Miriam Frech and Torsten Hechler for critical reading of the manuscript. Financial support of this work came from the German Research Foundation (DFG) in the frame of the priority programme “Genome functions and gene regulation in Archaea” (Pf 165/9-2) and DFG grant Pf 165/10-1.


  1. Baliga N, Goo Y, Ng W, Hood L, Daniels C, DasSarma S (2000) Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol Microbiol 36:1184–1185PubMedCrossRefGoogle Scholar
  2. Bell S, Cairns S, Robson R, Jackson S (1999) Transcriptional regulation of an archaeal operon in vivo and in vitro. Mol Cell 4:971–982PubMedCrossRefGoogle Scholar
  3. Chomczynski P, Sacchi N (1987) Single step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction. Anal Biochem 162:156–159PubMedCrossRefGoogle Scholar
  4. Coker J, DasSarma S (2007) Genetic transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA. BMC Genet 8:61. doi: 10.1186/1471-2156-8-61 PubMedCrossRefGoogle Scholar
  5. Englert C, Krüger K, Offner S, Pfeifer F (1992) Three different but related gene clusters encoding gas vesicles in halophilic archaea. J Mol Biol 227:586–592PubMedCrossRefGoogle Scholar
  6. Facciotti M, Reiss J, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe S, Hood L, Baliga N (2007) General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci USA 104:4630–4635PubMedCrossRefGoogle Scholar
  7. Ng W, Kothakota S, DasSarma S (1991) Structure of the gas vesicle plasmid in Halobacterium halobium: Inversion isomers, inverted repeats, and insertion sequences. J Bacteriol 173:1958–1964PubMedGoogle Scholar
  8. Ng W, Ciufo S, Smith T, Bumgarner R, Baskin D, Faust J, Hall B, Loretz C, Seto J, Slagel J, Hood L, DasSarma S (1998) Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome? Genome Res 8:1131–1141PubMedGoogle Scholar
  9. Ng W, Kennedy S, Mahairas G, Berquist B, Pan M, Shukla H, Lasky S, Baliga N, Thorsson V, Sbrogna J, DasSarma S et al (2000) Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci USA 97:12176–12181PubMedCrossRefGoogle Scholar
  10. Palmer JR, Daniels CJ (1995) Definition of an archaeal promoter. J Bacteriol 177:1844–1849PubMedGoogle Scholar
  11. Pfeifer F, Betlach M (1985) Genome organization in Halobacterium halobium: a 70 kb island of more (AT) rich DNA in the chromosome. Mol Gen Genet 198:449–455PubMedCrossRefGoogle Scholar
  12. Pfeifer F, Blaseio U (1989) Insertion elements and deletion formation in a halophilic archaebacterium. J Bacteriol 171:5135–5140PubMedGoogle Scholar
  13. Pfeifer F, Blaseio U (1990) Transposition burst of the insertion element family ISH27 in Halobacterium halobium. Nucleic Acids Res 18:6921–6925PubMedCrossRefGoogle Scholar
  14. Pfeifer F, Ghahraman P (1993) Plasmid pHH1 of Halobacterium salinarum: characterization of the replicon region, the gas vesicle gene cluster and insertion elements. Mol Gen Genet 238:193–200PubMedGoogle Scholar
  15. Pfeifer F, Weidinger G, Goebel W (1981) Characterization of plasmids in halobacteria. J Bacteriol 145:369–374PubMedGoogle Scholar
  16. Pfeifer F, Offner S, Krüger K, Ghahraman P, Englert C (1994) Transformation of halophilic archaea and investigation of gas vesicle synthesis. Syst Appl Microbiol 16:569–577Google Scholar
  17. Pfeifer F, Zotzel J, Kurenbach B, Röder R, Zimmermann P (2001) A p-loop motif and two basic regions in the regulatory protein GvpD are important for the repression of gas vesicle formation in the archaeon Haloferax mediterranei. Microbiology 147:63–73PubMedGoogle Scholar
  18. Pfeiffer F, Schuster SC, Broicher A, Falb M, Palm P, Rodewald K, Ruepp A, Soppa J, Tittor J, Oesterhelt D (2008a) Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 as compared to strain NRC-1. Genomics. doi:  10.1016/j.ygeno.2008.01.001
  19. Pfeiffer F, Broicher A, Gillich T, Klee K, Mejia J, Rampp M, Oesterhelt D (2008b) Genome information management and integrated data analysis with HaloLex. Arch Microbiol (this issue)Google Scholar
  20. Sambrook J, Russel DW (2001) Molecular cloning a laboratory manual. 3rd edn. Cold Spring Harbor, New YorkGoogle Scholar
  21. Scheuch S, Pfeifer F (2007) GvpD-induced breakdown of the transcriptional activator GvpE of halophilic archaea requires a functional p-loop and an arginine-rich region of GvpD. Microbiology 153:947–958PubMedCrossRefGoogle Scholar
  22. Thomm M (1996) Archaeal transcription factors and their role in transcription initiation. FEMS Microbiol Rev 18:159–171PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Katharina Teufel
    • 1
  • Anne Bleiholder
    • 1
  • Tim Griesbach
    • 1
  • Felicitas Pfeifer
    • 1
    Email author
  1. 1.Institute for Microbiology and GeneticsTechnische Universität DarmstadtDarmstadtGermany

Personalised recommendations