Nitrosopumilus maritimus genome reveals unique - de la Torre ...

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Acetyl-CoA carboxylase (Nmar_0272, 0273, 0274) Acetoacetyl-CoA -ketothiolase (Nmar_0841 or Nmar_1631) Malonyl-CoA reductase Malonate semialdehyde reductase (unknow n) 3-Hydroxypropionyl-CoA synthetase 3-Hydroxypropionyl-CoA dehydratase Acryloyl-CoA reductase (unknow n) Propionyl-CoA carboxylase (Nmar_0272, 0273, 0274) Methylmalonyl-CoA epimerase Methylmalonyl-CoA mutase (Nmar_0953, 0954, 0958) 3-Hydroxybutyryl-CoA dehydrogenase (Nmar_1028) Crotonyl-CoA hydratase (Nmar_1308) 4-Hydroxybutyryl-CoA dehydratase (Nmar_0207) 4-Hydroxybutyryl-CoA synthetase (Nmar_0206) Succinate semialdehyde reductase (Nmar_1110 or Nmar_0161) Succinyl-CoA reductase (Nmar_1608) Fig. S3. Proposed 3-hydroxypropionate/4-hydroxybutyrate cycle for autotrophic carbon fixation by N. maritimus. Walker et al. www.pnas.org/cgi/content/short/0913533107 4of5
A. 0.1 B. 100 90 52 Other Supporting Information Files Table S1 (DOC) Table S2 (DOC) Table S3 (DOC) Table S4 (DOC) Table S5 (DOC) Table S6 (DOC) 96 100 97 78 100 100 38 100 55 95 100 61 88 64 70 100 100 100 100 100 100 100 97 51 86 100 61 100 100 100 100 90 100 100 Giardia lamblia Entamoeba histolytica Leishmania major Cenarchaeum symbiosum Candidatus Nitrosopumilus maritimus Candidatus Korarchaeum cryptofilum Thermofilum pendens Caldivirga maquilingensis 100 94 100 Pyrobaculum calidifontis Pyrobaculum islandicum Pyrobaculum aerophilum Pyrobaculum arsenaticum Ignicoccus hospitalis Staphylothermus marinus Aeropyrum pernix Hyperthermus butylicus Metallosphaera sedula Sulfolobus solfataricus Thermococcus gammatolerans Thermococcus kodakarensis Pyrococcus furiosus Pyrococcus abyssi Pyrococcus horikoshii Methanopyrus kandleri 100 100 100 100 100 100 100 Trypanosoma cruzi Trypanosoma brucei Cryptosporidium parvum Theileria parva Plasmodium yoelii Plasmodium falciparum Arabidopsis thaliana Oryza sativa Dictyostelium discoideum Homo sapiens Anopheles gambiae Saccharomyces cerevisiae Schizosaccharomyces pombe Sulfolobus acidocaldarius Sulfolobus tokodaii Nanoarchaeum equitans Methanosphaera stadtmanae Methanothermobacter thermautotrophicus Methanocaldococcus jannaschii Methanococcus aeolicus 100 100 Methanococcus maripaludis Methanococcus vannielii Picrophilus torridus Ferroplasma acidarmanus Thermoplasma acidophilum Thermoplasma volcanium 100 100 100 Archaeoglobus fulgidus 69 Halobacterium sp Natronomonas pharaonis 71 Haloarcula marismortui 100 Halorubrum lacusprofundi 100 Haloquadratum walsbyi 100 Haloferax volcanii Methanocorpusculum labreanum 100 Methanoculleus marisnigri 75 Candidatus Methanoregula 82 Methanospirillum hungatei Methanosaeta thermophila Methanococcoides burtonii 100 Methanosarcina barkeri 100 Methanosarcina acetivorans 100 Methanosarcina mazei 1.00 Saccharomyces cerevisiae Dictyostelium discoideum Oryza sativa Candidatus Korarchaeum cryptofilum Candidatus Nitrosopumilus maritimus 1.00 Cenarchaeum symbiosum 0.88 Pyrobaculum aerophilum 1.00 1.00 Thermofilum pendens 1.00 1.00 Aeropyrum pernix Hyperthermus butylicus 0.88 1.00 1.00 Sulfolobus acidocaldarius Metallosphaera sedula Nanoarchaeum equitans Thermococcus kodakarensis 1.00 1.00 Pyrococcus abyssi Methanopyrus kandleri 1.00 1.00 Methanothermobacter thermautotrophicus 1.00 Methanosphaera stadtmanae 1.00 1.00 Methanocaldococcus jannaschii Methanococcus maripaludis Thermoplasma volcanium 1.00 1.00 Ferroplasma acidarmanus 1.00 Archaeoglobus fulgidus Haloarcula marismortui 1.00 1.00 Natronomonas pharaonis 1.00 1.00 Methanosarcina mazei Methanosaeta thermophila 0.70 Methanospirillum hungatei 0.1 1.00 Methanocorpusculum labreanum Eucarya Thaumarchaeota Korarchaeota Thermoproteales Desulfurococcales Sulfolobales Nanoarchaeota Thermococcales Methanopyrales Methanobacteriales Eucarya Methanococcales Thermoplasmatales Archaeoglobales Halobacteriales Methanomicrobiales Methanosarcinales Korarchaeota Thaumarchaeota Thermoproteales Desulfurococcales Sulfolobales Nanoarchaeota Thermococcales Methanopyrales Methanobacteriales Methanococcales Thermoplasmatales Archaeoglobales Halobacteriales Methanosarcinales Methanomicrobiales Fig. S4. (A) Maximum-likelihoodphylogenyofGroup1Archaea. The phylogeny was inferred using an alignment of concatenated R-proteins (66 taxa, 6,142 positions). WAG+Inv+Gamma (4 classes); 100 replicates. (B) BayesiantreeofmesophilicGroup1Archaea inferred using an alignment of concatenated Rproteins (29 taxa, 6,142 positions). Mixed model + Gamma (4 classes); 100 replicates. Walker et al. www.pnas.org/cgi/content/short/0913533107 5of5 Crenarchaeota Euryarchaeota Crenarchaeota Euryarchaeota
Page 1 and 2: Nitrosopumilus maritimus genome rev
Page 3 and 4: ammonia oxidation. There are two hy
Page 5 and 6: Fig. 3. Comparison of N. maritimus
Page 7 and 8: Supporting Information Walker et al
Page 9: Fig. S2. Archaeal ammonia monooxyge
Page 13 and 14: Supplemental Table 2: Predicted coo
Page 15 and 16: Supplemental Table 3: Gene predicti
Page 17 and 18: Nmar_tR26 1,630,610 1,630,537 ProGG
Page 19 and 20: Supplemental Table 4: Gene predicti
Page 21 and 22: Nmar_0258 CENSYa_1705 82 227,624 22
Page 29 and 30: Nmar_1303 CENSYa_0131 86 1,193,261
Page 35 and 36: Molybdopterin-guanine dinucleotide
Page 37 and 38: Nmar0935 DeepAntEC39 f 815,847 816,
Page 39 and 40: Nmar0101 EQ085329 r 91,543 93,711 A
Page 41 and 42: Nmar0436 EQ085799 f 386,930 387,319
Page 43 and 44: Nmar0982 EP710054 r 859,116 859,526
Page 45 and 46: Nmar1297 EQ086682 f 1,187,165 1,188

Nitrosopumilus maritimus genome reveals unique - de la Torre ...

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