Microarray analysis in the archaeon Halobacterium salinarum strain R1.

<h4>Background</h4>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...

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Autores principales:	Jens Twellmeyer, Andy Wende, Jan Wolfertz, Friedhelm Pfeiffer, Markus Panhuysen, Alexander Zaigler, Jörg Soppa, Gerhard Welzl, Dieter Oesterhelt
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2007
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/08581d0c4fa84b69b3917a8bb1f98c84
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spelling	oai:doaj.org-article:08581d0c4fa84b69b3917a8bb1f98c842021-11-25T06:10:39ZMicroarray analysis in the archaeon Halobacterium salinarum strain R1.1932-620310.1371/journal.pone.0001064https://doaj.org/article/08581d0c4fa84b69b3917a8bb1f98c842007-10-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0001064https://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusion/significance</h4>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.Jens TwellmeyerAndy WendeJan WolfertzFriedhelm PfeifferMarkus PanhuysenAlexander ZaiglerJörg SoppaGerhard WelzlDieter OesterheltPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 2, Iss 10, p e1064 (2007)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jens Twellmeyer Andy Wende Jan Wolfertz Friedhelm Pfeiffer Markus Panhuysen Alexander Zaigler Jörg Soppa Gerhard Welzl Dieter Oesterhelt Microarray analysis in the archaeon Halobacterium salinarum strain R1.
description	<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusion/significance</h4>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.
format	article
author	Jens Twellmeyer Andy Wende Jan Wolfertz Friedhelm Pfeiffer Markus Panhuysen Alexander Zaigler Jörg Soppa Gerhard Welzl Dieter Oesterhelt
author_facet	Jens Twellmeyer Andy Wende Jan Wolfertz Friedhelm Pfeiffer Markus Panhuysen Alexander Zaigler Jörg Soppa Gerhard Welzl Dieter Oesterhelt
author_sort	Jens Twellmeyer
title	Microarray analysis in the archaeon Halobacterium salinarum strain R1.
title_short	Microarray analysis in the archaeon Halobacterium salinarum strain R1.
title_full	Microarray analysis in the archaeon Halobacterium salinarum strain R1.
title_fullStr	Microarray analysis in the archaeon Halobacterium salinarum strain R1.
title_full_unstemmed	Microarray analysis in the archaeon Halobacterium salinarum strain R1.
title_sort	microarray analysis in the archaeon halobacterium salinarum strain r1.
publisher	Public Library of Science (PLoS)
publishDate	2007
url	https://doaj.org/article/08581d0c4fa84b69b3917a8bb1f98c84
work_keys_str_mv	AT jenstwellmeyer microarrayanalysisinthearchaeonhalobacteriumsalinarumstrainr1 AT andywende microarrayanalysisinthearchaeonhalobacteriumsalinarumstrainr1 AT janwolfertz microarrayanalysisinthearchaeonhalobacteriumsalinarumstrainr1 AT friedhelmpfeiffer microarrayanalysisinthearchaeonhalobacteriumsalinarumstrainr1 AT markuspanhuysen microarrayanalysisinthearchaeonhalobacteriumsalinarumstrainr1 AT alexanderzaigler microarrayanalysisinthearchaeonhalobacteriumsalinarumstrainr1 AT jorgsoppa microarrayanalysisinthearchaeonhalobacteriumsalinarumstrainr1 AT gerhardwelzl microarrayanalysisinthearchaeonhalobacteriumsalinarumstrainr1 AT dieteroesterhelt microarrayanalysisinthearchaeonhalobacteriumsalinarumstrainr1
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Microarray analysis in the archaeon Halobacterium salinarum strain R1.

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