Introduction halobacteria Halobacterium salinarum Haloferax mediterranei Haloarcula marismortui Halococcus saccharolyticus 1988 1992 2001 2004 H. salinarum 1988 Haloferax volcanii 1990 Dunaliella salina 2006 Microcoleus chthonoplastes 1995 Haloferax volcanii 1990 Natronomonas pharaonis 2005 H. salinarum Halobacterium 1973 1976 2004 2006b 2002 2005 2003 2004 2006 2005 2004 2006 1 H. salinarum 2000 2008 http://www.halolex.mpg.de H. marismortui 2004 N. pharaonis 2005 Haloquadratum walsbyi 2006 Table 1 Overview of the currently sequenced haloarchaea  H. salinarum a H. marismortui H. walsbyi N. pharaonis Gene identifier VNG/OE rrn, pNG HQ NP Salt optimum [M] 4–5 M 4.5 M 3.3 M 3.5 M (pH 8.5) Isolation Salted fish Dead Sea (Israel) Solar saltern (Spain) Soda lake (Egypt) Main research interests Rhodopsins, signal transduction Versatile nitrogen metabolism Square-shaped cells, halomucin Haloalkaliphilicity, respiratory chain Genome size [Mb] 2.61/2.72 4.37 3.24 2.80 # Plasmids 2/4 8 (incl. CHRII) 1 2 %GC chromosome 68.0 62.4 47.9 63.4 rRNA operons 1 3 2 1 Fla genes (motility) Yes Yes No Yes # Transducer genes 18 21 (18) 0 19 # Rhodopsin genes (bop, hop, sop) 4 (1,1,2) 6 (3,1,2) 3 (2,1,0) 2 (0,1,1) a H. salinarum 2000 2008 http://www.halolex.mpg.de H. salinarum Materials and methods Metabolic reconstruction procedure H. salinarum 2004 H. salinarum H. salinarum http://www.halolex.mpg.de H. salinarum H. salinarum Comparative analysis of the complete haloarchaeal gene sets H. salinarum N. pharaonis, H. walsbyi H. marismortui N. pharaonis H. salinarum H. salinarum N. pharaonis N. pharaonis H. salinarum N. pharaonis H. salinarum H. salinarum E −20 Results and discussion H. salinarum http://www.halolex.mpg.de 2 H. salinarum H. marismortui H. walsbyi, N. pharaonis H. salinarum N. pharaonis Glycolytic pathways 1 H. salinarum H. marismortui H. walsbyi 1988 1992 2003 H. marismortui H. walsbyi 2005 H. salinarum Halobacterium 1969 1988 N. pharaonis Fig. 1 reaction arrows H. salinarum green red H. marismortui H. walsbyi N. pharaonis H. salinarum green red H. salinarum bold arrows green red H. salinarum green arrows with red border H. salinarum red arrows with green border asterisks H. salinarum E d  H. marismortui 1992 Haloarcula 2004 Embden-Meyerhof pathway and gluconeogenesis 1988 1992 Thermococcus, Pyrococcus Thermoproteus 1994 1997 1992 1994a b H. marismortui H. salinarum 1988 2006 1990 1998 1988 H. salinarum 1998 H. salinarum 1987 Entner-Douderoff pathway 1992 H. vallismortis 1992 Sulfolobus Thermoplasma 2005 Sulfolobus 2005 2005 H. salinarum H. marismortui H. walsbyi d gnaD kdgK kdgA kdgK H. salinarum 1996 N. pharaonis H. marismortui H. walsbyi Haloferax alicantei kdgK kdgA Halobacterium Sulfolobus Thermoplasma H. salinarum H. salinarum 1990 1999 1988 Oxidative pentose phosphate pathway 6 5 1969 Pentose metabolism 6 3 5 Methanococcus jannaschii Thermoplasma  2005 Methanocaldococcus jannaschii 2005 M. jannaschii 2006 2005 d Thermoplasma 2005 4 Pyrococcus abyssi l 2004 2 H. mediterranei H. salinarum 1988 1994 2 d 2004 N. pharaonis N. pharaonis 2007 2 2 2007 Glycerol metabolism Dunaliella 1977 2003 1988 1999 sn N. pharaonis Dunaliella 1999 H. salinarum 1988 2003 2006 H. walsbyi 2006 Pyruvate metabolism and tricarboxylic acid cycle Pyruvate metabolism porAB 1981a b H. salinarum 1998 1994 1998 2000 H. marismortui H. walsbyi 2006 H. salinarum 1994 1998 H. salinarum 1994 1998 H. salinarum 1994 M. jannaschii 2006a M. jannaschii Tricarboxylic acid cycle 1999 H. salinarum 1969 1972 1981a b 1985 1998 porAB korAB 1981a b Thermoplasma acidophilum 2004 Haloferax volcanii 2001 N. pharaonis H. walsbyi H. marismortui Halobacterium 1969 Nucleotide metabolism De novo synthesis of nucleotides 2 purN/purH purP 2005 purO 2002 Fig. 2 linked boxes 3 9 10 unfilled boxes question marks  Archaeal type III RuBisCO functions in AMP metabolism 2 2007 1994 1997 N. pharaonis H. salinarum 2007 N. pharaonis 2 Lipid metabolism H. salinarum 20 30 40 40 60 1976 1985 1976 3 H. salinarum 50 20 1976 1973 14, 16, 18 H. salinarum 1994 H. salinarum N. pharaonis 20 20 20 25 1984 Fig. 3 green red bold H. salinarum boxes H. marismortui H. walsbyi N. pharaonis H. salinarum green red B A Superscript “a” 5 2 1986  1986 1999 De novo synthesis of isoprenoids (mevalonate pathway) 5 3 2000 2004 2006b 3 N. pharaonis H. salinarum H. salinarum 1986 2 5 trans cis H. salinarum Synthesis of carotenoids and retinal 40 50 1976 H. salinarum 2002 20 H. walsbyi H. marismortui 2006 H. salinarum N. pharaonis brp blh 2001 Fatty acid metabolism 1994 H. salinarum 2000 1989 Natronomonas Haloarcula H. salinarum H. walsbyi N. pharaonis 14 H. salinarum 14 18 14 2006 . Natronomonas Amino acid synthesis Haloarcula hispanica 1999 H. salinarum 1973 1976 H. salinarum H. salinarum H. salinarum H. salinarum 2002 2002 H. salinarum 1986 1994 1998 1989 1 H. marismortui N. pharaonis H. walsbyi N. pharaonis 2005 2006 2005 Glutamate family (glutamate, glutamine, proline, arginine) Halobacterium 1998 1986 Natronomonas Halobacterium Haloarcula Haloquadratum Halobacterium + + 1987 1989 1990 1999 2002 N. pharaonis H. walsbyi H. marismortui 2005 2002 1997 l proCBA Natronomonas Haloquadratum Halobacterium Haloarcula H. salinarum 1998 putA putA proABC putA H. salinarum H. marismortui N. pharaonis H. walsbyi M. jannaschii 2001 Natronomonas, Haloquadratum Haloarcula argXCBDEF argA Halobacterium Aspartate family (aspartate, alanine, asparagine, threonine, methionine, lysine) Halobacterium 1994 H. salinarum 1989 l l l O l M. jannaschii O l 2003 O l O l O l O l  metE H. salinarum H. hispanica 1999 Natronomonas, Haloquadratum Haloarcula dapABD dapC argD lysA argG dapE, dapF Haloarcula Natronomonas Halobacterium dap Serine family (serine, glycine, cysteine) serA serB serC Methanococcales 2007 Natronomonas, Haloquadratum Haloarcula Halobacterium H. salinarum H. walsbyi Halobacterium Halobacterium O l O cysE cysK M. jannaschii cysE cysK 2003 M. jannaschii 2005 2003 cysD cysN cysC, cysH Aeropyrum pernix H. salinarum Biosynthesis of branched chain amino acids (valine, leucine, isoleucine) Natronomonas, Haloquadratum Haloarcula Halobacterium H. hispanica 1999 H. hispanica 1999 mamABC H. salinarum H. marismortui . Halobacterium 1994 Halobacterium Biosynthesis of aromatic amino acids (phenylalanine, tyrosine, tryptophan, histidine) 4 3 Thermoplasma 2005 l 4 6 2004 H. salinarum 1989 d 2006 2006 H. salinarum 1986 1989 M. maripaludis 2004 ior porAB korAB 1981a b H. salinarum 1986 Amino acid degradation Glutamate and aspartate degradation H. salinarum H. marismortui . mamABC E. coli Clostridium Treponema 2001 H. hispanica 1999 Arginine metabolism H. marismortui H. salinarum 1980 H. salinarum arcRACB 1996 2002b 2000 2002b Branched-chain amino acid degradation 2004 Aromatic amino acid degradation H. salinarum H. marismortui hutUGIH A. pernix H. salinarum H. walsbyi l 2005 M. jannaschii Cofactor metabolism thiI, moaA 2002a 2006 2007 . N. pharaonis 2005 + + pdxS/pdxT B. subtilis 2005 N. pharaonis bioA H. marismortui bioA bioD H. salinarum H. walsbyi N. pharaonis thiM thiE tenA N. pharaonis tenA thiC thiN thiD thiE 2003 H. salinarum 2004 Halobacterium 1973 + + 2002 1981a b 2003 1976 1998 1997 1997 2005 1994 Heme and cobamide synthesis men hem hemE M. barkeri 2006 2006 Halobacterium 12 2003 Pseudomonas denitrificans cob Salmonella typhimurium cbi/cob Bacillus megaterium 2003 S. typhimurium cbiK, B. megaterium cbiX P. denitrificans cobN cobN cbiX Halobacterium 2003 cob P. denitrificans cobG, cobF cobK S. typhimirium cobJ cobP S. typhimirium cobU) cobP cbiZ cobY 2003 2004 cobZ 2006 H. salinarum cobC Salmonella hemCXD Natronomonas 2006 Folate synthesis p 4 folE, folB folK H. marismortui. folE 2006 2007 folB folK pabAB pabC pabA H. salinarum de novo pab M. maripaludis 2006 Fig. 4 H. marismortui H. walsbyi N. pharaonis H. salinarum H. volcanii green red  folP folC 4 . folA H. salinarum H. salinarum 2004 2007 thyA thyX folA H. salinarum H. marismortui H. walsbyi H. marismortui Conclusions H. marismortui H. walsbyi N. pharaonis H. salinarum Halobacterium H. salinarum 2004 2007 H. marismortui H. walsbyi H. salinarum d N. pharaonis 2007 cobC folA 2008 H. salinarum 1969 1988 1 Halobacterium Electronic supplementary material Below is the link to the electronic supplementary material.
 Supplementary Material S1 Supplementary Material S2 Supplementary Material S3 Supplementary Material S4