Hot Transcriptomics

Table 1

A list of different archaeal transcriptome publications. This table shows that transcriptome studies are mostly done to elucidate metabolic processes or the behaviour of different archaea in stress situations. The publications are sorted by subject. Per subject the publications are sorted by year of publication. We included some environmental studies because they give a crucial insight in the ecological function of archaeal species. We excluded some of these publications because in our view they focused more on nonarchaeal species, which is a subject not related to this article. The studies referring to thermophiles are in bold. The studies more described in this paper in more detail are marked with an asterisk next to the reference.

Organism	Subject studied	Reference
	Metabolism
Pyrococcus furiosus	Sulfur metabolism	[24]*
Halobacterium salinarum  NRC-1	Adaptation to phototrophy	[25]
Haloferax volcanii	Central carbon metabolism	[26]
Pyrococcus furiosus	Central carbon metabolism	[27]*
Halobacterium salinarum NRC-1	Anaerobic respiration	[28]
Methanosarcina mazei	Metabolism of methanogenic substrates	[29]
Sulfolobus solfataricus	Central carbon metabolism	[30]
Sulfolobus solfataricus	Pentose metabolism	[7]*
Methanosarcina barkeri	Methanogen metabolism/methods	[31]
Methanosarcina mazei	Nitrogen metabolism and regulation	[32]
Pyrococcus furiosus	Starch metabolism	[33]
Pyrococcus furiosus	Metabolism of elemental sulfur	[34]
Halobacterium salinarum R1	Adaptation to phototrophy	[35]
Methanosarcina acitovorans	Acetate and methanol metabolism	[36]
Environmental array	Ammonium oxidation	[37]
Metallosphaera sedula	Electron transport chain	[38]
Methanosarcina	Methanogenesis	[39]
Pyrobaculum aerophilum	Terminal electron acceptor studies	[40]
Thermoproteus tenax	Central carbohydrate metabolism	[41]
Halobacterium salinarum R1	Phosphate-dependent behaviour	[42]
Halobacterium salinarum NRC-1	Global response to nutrient availability	[43]
Haloferax volcanii	D-Xylose metabolism	[44]
Methanosarcina mazei	Response to nitrogen availability	[45]
Metallosphaera sedula	Auto- hetero- and mixotrophic growth	[21]
Metallosphaera sedula	Bioleaching	[46]
	Stress
Pyrococcus furiosus	Heat shock response	[47]*
Pyrococcus furiosus	Cold shock response	[48]
Halobacterium salinarum NRC-1	UV irradiation	[49]
Methanocaldococcus janaschii	Heat and cold shock	[50]
Methanosarcina barkeri	Heat shock and air exposure	[51]
Methanocaldococcus janaschii	Pressure stress	[52]
Pyrococcus furiosus	Response to gamma irradiation	[53]
Methanosarcina mazei	Salt adaptation	[54]
Methanococcus maripaludis	H-limitation and growth rate	[55]
Halobacterium salinarum NRC-1	Response to change in temperature and salinity	[56]
Sulfolobus solfataricus	UV irradiation	[57]
Sulfolobus solfataricus; S. acidocaldarius	UV irradiation	[58]
Sulfolobus solfataricus	Heat Shock Response	[59]*
Halobacterium salinarumNRC-1	UV irradiation	[25]
Sulfolobus solfataricus	Oxygen stress	[60]
Sulfolobus solfataricus	Oxygen stress	[61]
Methanococcoides burtonii	Heat stress	[62]
Thermococcus kodakaraensis	Heat stress	[63]
Pyrococcus furiosus	Heat stress	[64]
Sulfolobus solfataricus	Heat stress	[65]
Pyrococcus furiosus	Oxidative stress	[66]
Methanohalophilus portucalensis	Hypo- and Hyper-salt stress	[67]
	Replication
Sulfolobus solfataricus; S. acidocaldarius	Origin of replication	[68]*
Halobacterium salinarum NRC-1	Cell cycle regulation	[69]
Pyrococcus abyssi	Origin of replication	[70]
Sulfolobus acidocaldarius	Cell cycle	[20]*
	Various
Environmental array	Methanotroph diversity in landfills	[71]
Pyrococci	Genomic DNA hybridization	[72]
Sulfolobus solfataricus; S. acidocaldarius	RNA decay	[73]
Methanococcus maripaludis	Mutant studies	[74]
Haloferax volcanii	Promoter studies	[75]
Thermococcus kodakaraensis	Promotor studies	[76]
Thermococcus kodakaraensis	Archaeal operon prediction	[77]
Haloferax volcanii	Deletion mutant analysis	[78]
Environmental array	Detection of acidophilic activity	[79]
Sulfolobus solfataricus	Viral infection	[80]*
Sulfolobus	Genomic hybridizations	[81]
Sulfolobus	Transcription bias near OriC	[82]
Sulfolobus solfataricus	Single base resolution map of the genome	[83]*
Environmental array	Antarctic soil community	[84]
0Methanosarcina acetivorans	Regulation of genes	[85]
Halobacterium salinarum R1	Control of multiple genes by regulatory proteins	[86]
Haloacterium salinarum NRC-1	Physiological readjustments during growth	[87]
Environmental array	Methanogens in cattle excreta	[88]
Environmental array	Gene transfer	[89]