title: Microarray analysis in the archaeon Halobacterium salinarum strain R1.
abstract: BACKGROUND
  Phototrophy of the extremely halophilic archaeon Halobacterium salinarum was explored for decades. The research was mainly focused on the expression of bacteriorhodopsin and its functional properties. In contrast, less is known about genome wide transcriptional changes and their impact on the physiological adaptation to phototrophy. The tool of choice to record transcriptional profiles is the DNA microarray technique. However, the technique is still rarely used for transcriptome analysis in archaea.
  
  
  RESULTS
  We developed a whole-genome DNA microarray based on our sequence data of the Hbt. salinarum strain R1 genome. The potential of our tool is exemplified by the comparison of cells growing under aerobic and phototrophic conditions, respectively. We processed the raw fluorescence data by several stringent filtering steps and a subsequent MAANOVA analysis. The study revealed a lot of transcriptional differences between the two cell states. We found that the transcriptional changes were relatively weak, though significant. Finally, the DNA microarray data were independently verified by a real-time PCR analysis.
  
  
  CONCLUSIONS
  This is the first DNA microarray analysis of Hbt. salinarum cells that were actually grown under phototrophic conditions. By comparing the transcriptomics data with current knowledge we could show that our DNA microarray tool is well applicable for transcriptome analysis in the extremely halophilic archaeon Hbt. salinarum. The reliability of our tool is based on both the high-quality array of DNA probes and the stringent data handling including MAANOVA analysis. Among the regulated genes more than 50% had unknown functions. This underlines the fact that haloarchaeal phototrophy is still far away from being completely understood. Hence, the data recorded in this study will be subject to future systems biology analysis.
authors.affiliation: Max-Planck-Institute of Biochemistry, Membrane Biochemistry, Martinsried, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Twellmeyer
authors.forename: Andy
authors.initials: A
authors.lastname: Wende
authors.forename: Jan
authors.initials: J
authors.lastname: Wolfertz
authors.forename: Friedhelm
authors.initials: F
authors.lastname: Pfeiffer
authors.forename: Markus
authors.initials: M
authors.lastname: Panhuysen
authors.forename: Alexander
authors.initials: A
authors.lastname: Zaigler
authors.forename: Jörg
authors.initials: J
authors.lastname: Soppa
authors.forename: Gerhard
authors.initials: G
authors.lastname: Welzl
authors.forename: Dieter
authors.initials: D
authors.lastname: Oesterhelt
mesh_terms: D019843:Archaeal Proteins / Q000235:genetics; D001671:Biochemistry / Q000379:methods; D017931:DNA Primers / Q000737:chemistry; D018076:DNA, Complementary / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D019617:Halobacterium salinarum / Q000235:genetics* / Q000378:metabolism*; D008027:Light; D015233:Models, Statistical; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000737:chemistry; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013050:Spectrometry, Fluorescence; D014158:Transcription, Genetic
chemical_list: D019843:Archaeal Proteins; D017931:DNA Primers; D018076:DNA, Complementary; D012313:RNA