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Tree scale: 1 Methanopyrus sp. Methanopyrus kan KOL6 dleri Thermococcus eur Thermococcus Thermococcus gam Thermococcus Thermococcus gor Thermococcus Thermococcus thio Thermococcus Thermococcus gua Thermococcus Thermococcus sp. Thermococcus Thermococcales a sp. Thermococcus Thermococcus rad Thermococcus Thermococcus zill Thermococcus Thermococcus pep Thermococcus Thermococcus cele Thermococcus Thermococcus cele Thermococcus Thermococcus nau Thermococcus Thermococcus chi kod Thermococcus Thermococcus sp. Thermococcus Thermococcus pie Thermococcus Palaeococcus ferro Palaeococcus Pyrococcus furiosu onn Thermococcus Palaeococcus paci Palaeococcus Thermococcus sp. Thermococcus sp. Thermococcus Thermococcus sp. clef Thermococcus Thermococcus pro Thermococcus Fervidobacterium Thermococcus sib bar Thermococcus Thermococcus sib Thermococcus pac Thermococcus Methanothermus f Pyrococcus horiko Thermococcus par sp. Thermococcus Pyrococcus kukulk Thermococcus barThermococcus sp. Thermococcus bar Thermococcus lito Thermococcus Thermococcus lito Thermococcus sp. ythermalis Pyrococcus sp. ST sicu Thermococcus Pyrococcus sp. NA matolerans Pyrococcus abyssi gonarius ymasensis reducens Pyrococcus furiosu EXT12c Desulfurococcales P6 Desulfurococcales rchaeon 44_46 Pyrococcus yayan iotolerans igii AM4 tili r tonophagus tonophilus ricrescens Aeropyrum camini Aeropyrum akarensis zophilus s DSM 3638 Sulfolobus islandic ficus 5-4 40_45 urineus Sulfolobus islandic philus Sulfolobus islandic thailandense 2319x1 fundus tensis Sulfolobus islandic ervidus iricus ossii Sulfolobus islandic iricus 4557 Sulfolobus islandic shii ificus Sulfolobus islandic alvinellae Sulfolobus islandic Candidatus Acidia Sulfolobus islandic Sulfolobus Sulfolobussp. JCM solfata EP1 hospita Ignicoccus Sulfolobus islandic anii ophilus ophilus ralis ralis 04 Sulfolobus shibata PK 2 li Desulfurococcales Ignicoccus islandi Ignicoccus Sulfolobus sp. A20 ex4484 archaeon Acidianus sulfidivo s ex4484 archaeon Ignicoccus hospita Ignicoccus SulfolobalesAcidianus archa manzae osii MetallosphaeraSulfolobales ye archa pernix Aeropyrum Metallosphaera ha AcidianusAcidianus hospital hospital 12091 JCM = SY1 Hyperthermus but Hyperthermus Metallosphaera se occul Pyrodictium nus copahuensis occul Pyrodictium Metallosphaera cu usus Sulfolobales archa usus Thermogladius cal Thermogladius usus fumarii Pyrolobus ricus delan Pyrodictium Sulfolobus acidoca Acidianus brierley 16833 usus us delan Pyrodictium us h Staphylothermus Sulfolobus sp. SCG KIN4/I lis archaeon ex4484 archaeon Desulfurococcus m Desulfurococcus e a Desulfurococcus Thermosphaera ag Thermosphaera Staphylothermus m Staphylothermus Sulfolobus acidoca m Desulfurococcus Sulfolobus acidoca a Desulfurococcus Desulfurococcus a Desulfurococcus rans cus _217_2 llowstonensis _217_1 eoneon AZ1 AZ1nsis konensis Desulfurococcales lis Ignisphaera aggre Ignisphaera K1 isis Desulfurococcacea eon SCGCSulfurisphaera AB-777_ tok prinadula ylicus Desulfurococcacea tum ldarius SUSAZ tum Ignicoccus hospita C AB-777_L09 Desulfurococcacea Ignicoccus islandi i derae eyi eyi mylolyticus ldarius ellenicus mylolyticus _58 ldarius ucosus gregans mylolyticus Desulfurococcacea ucosus Desulfurococcales arinus archaeon ex4484 archaeon gans DSM 17230 DSM gans Ignisphaera aggre J03 odaii NZ3(B archaeon e e archaeon AG1 archaeon e cuslis AG1 archaeon e Desulfurococcacea Fervidicoccus font Fervidicoccus Desulfurococcacea archaeone archaeon ex4484 NZ3(B Aciduliprofundum Sulfolobales archa Sulfolobales _42 gans DSM 17230 sp. Fervidicoccus ) Fervidicoccus font Fervidicoccus Desulfurococcus a JCM sp. Sulfolobus Desulfurococcus a e archaeon AG1 Desulfurococcus a e archaeon AG1 sp. _42) Kam940 is eon SCGC AB-777_ SCGC eon Desulfurococcales Desulfurococcus m Thermosphaera ag mylolyticus mylolyticus is Staphylothermus m A20 sp. Sulfolobus 16833 Staphylothermusmylolyticus h solfata Sulfolobus archaeon ex4484 islandic Sulfolobus J03 ucosus islandic Sulfolobus gregans islandic Sulfolobus Thermogladius cal islandic Sulfolobus Sulfolobus islandic Sulfolobus ellenicusarinus islandic Sulfolobus Sulfolobus islandic Sulfolobus _58 ricus us derae us us HVE10/4 us us us uncultured Acidilo us us us us uncultured Acidilo us uncultured Acidilo Sulfolobus islandic Sulfolobus islandic odaii Acidilobus saccharbus sp. JCHS SulfolobusSulfolobus islandicislandic C AB-777_G05 Acidilobusbus sp. sp. 7A MG ldarius DSM 639 Caldisphaera lagu bus sp. CIS ldarius ldarius SUSAZ ldarius DSM 639 Caldisphaeraovorans sp. SulfurisphaeraSulfolobus sp. tok SCG Caldisphaeranensis sp. Sulfolobus acidocaacidoca Aeropyrum camini Sulfolobus acidocallowstonensis Aeropyrum pernix Sulfolobus acidoca prina konensis SY1 = JCM 12091 MetallosphaeraMetallosphaera ye dulacu K1 Metallosphaera ha Metallosphaerai se Pyrodictium occul eon AZ1 Pyrodictium occul Acidianus brierley eon AZ1 Sulfolobales archa nus copahuensis Pyrodictium delantum Sulfolobales archa Pyrodictium delantum Candidatus Acidia rans Hyperthermus but eyi Acidianus sulfidivonsis Hyperthermus but eyi Acidianus manzaeis Acidianus hospital ylicus DSM ylicus5456 Acidianus hospitalis Pyrolobus fumarii FervidicoccusFervidicoccus font font is Kam940is Fervidicoccus sp. Candidatus Marsar chaeota G2 archaeon OSP_D Candidatus Marsarchaeota G2 archaeon ECH_B_SAG-C16 chaeota G2 archaeon ECH_B_3 Candidatus Marsar on ECH_B_2 eon ex4572_27 Candidatus Marsarchaeota G2 archae Candidatus Geothermarchaeota archa 8 chaeota G2 archaeon ECH_B_SAG-F0on OSP_D Thermofilum sp. ex4484_82 Candidatus Marsar chaeota G1 archae on BE_D Candidatus Marsar chaeota G1 archae Thermofilum sp. NZ13 Candidatus Marsar Thermofilum uzonense Thermofilum uzonense haeota archaeon Thermofilum Candidatus Korarc Thermofilum pend Thermofilum pendens Hrk 5 ens Candidatus Bathya Candidatus Bathyarchaeota archaeon rchaeota archaeon ex4484_135 Desulfurococcales B24 archaeon ex4484 _217_2 Candidatus Krypto CandidatusCandidatus Krypto Krypto Candidatus Krypto nium thompsoni Candidatus Krypto nium thompsoni bacter tengchonge bacter tengchonge r bescii bacter tengchonge r bescii bacter tengchonge Caldicellulosirupto r bescii Thermocladium sp nsis Caldicellulosirupto Caldivirga sp. MU8 nsis Caldicellulosiruptor owensensis Caldivirga maquili nsis r hydrothermalis Vulcanisaeta therm nsis Caldicellulosiruptor kronotskyensisr lactoaceticusr acetigenus Vulcanisaeta sp. E . ECH_B Vulcanisaeta mout 0 Caldicellulosirupto r kristjanssoniir obsidiansis Vulcanisaeta distr ngensis CaldicellulosiruptoCaldicellulosirupto Caldicellulosirupto r naganoensisr sp. F32 ophila Caldicellulosirupto r danielii B80 Caldicellulosiruptor saccharolyticusN r morganiisp. Dictyoglomus Thermoproteus te novskia Thermoproteus uzibuta CaldicellulosiruptoCaldicellulosirupto Thermoproteus sp subterraneus subterraneus Pyrobaculum calid Caldicellulosirupto TB sp. Thermotoga subterraneusTB sp. Thermotoga CaldicellulosiruptoCaldicellulosirupto Thermotoga Pyrobaculum sp. W nax Thermotoga sp. Ce sp. Thermotoga Pyrobaculum neut Z13-RE01 Thermotoga oniensis Thermotoga marit Thermotoga Thermotoga sp. RQ sp. Thermotoga PyrobaculumPyrobaculum arse islan . JCHS_4 Caldanaerobacter petro Thermotoga Pyrobaculum ogun Thermotoga sp. M sp. Thermotoga Pyrobaculum ferri Caldanaerobacter napht Thermotoga Pyrobaculum aero ifontis JCM 11548 Caldanaerobacter XY761 YP3.1.4.1 Thermotoga neapo Thermotoga P30 Thermotoga neapo Thermotoga rophilum V24Sta Thermotoga sp. RQ sp. Thermotoga ll2 Thermotoga sp. SG sp. Thermotoga Thermotoga sp. KO sp. Thermotoga ima naticumdicum DSM 1351 2 Candidatus Pacear phila reducensiense TE7 Thermotoga sp. 44 sp. Thermotoga c24 Thaumarchaeota a hophila philum str. IM2 Thermosipho atlan Thermosipho litana LA10 litana Thermosipho afric Thermosipho litana archaeon HR02 7 4 1 Candidatus Caldia L6 Candidatus Caldiachaeota archaeon Spirochaetes bact Spirochaetes rchaeon ex4484_1 84_232 anus ticus rchaeum subterraex4484_31 Geoglobus ahanga Geoglobus Ferroglobus placid Ferroglobus Thermovibrio ammbacterium HR19 rchaeum subterra Archaeoglobus ven Archaeoglobus Desulfurobacteriu Archaeoglobus pro Archaeoglobus 21 Geoglobus acetivo Geoglobus erium GWB1_36_1 erium Archaeoglobus ful Archaeoglobus Archaeoglobus ful Archaeoglobus Archaeoglobus ful Archaeoglobus Desulfurobacteriu Archaeoglobus ful Archaeoglobus Desulfurobacteriu Desulfurobacteriu bacterium HR35 neum Candidatus Bathya Candidatus Thermosulfidibact Aigarchaeota arch Aigarchaeota bacterium HR37 neum ri onificans us m thermolithotrop Candidatus Korarc Candidatus Candidatus Korarc Candidatus Aciduliprofundum Archaeoglobus sul Archaeoglobus Aciduliprofundum eficus rans 3 fundus Aciduliprofundum Candidatus Korarc Candidatus m atlanticum gidus DSM 4304 DSM gidus m indicum gidus DSM 4304 DSM gidus Hydrogenivirga spbacterium HR17 gidus Aquifex aeolicus V m sp. TC5-1 gidus Aquifex aeolicus Nanoarchaeum eq Nanoarchaeum ThermotogaPseudothermotoga caldif Pseudothermotoga er takaii Thermotoga sp. 50 aeon NZ13_MG1 aeon rchaeota archaeon rchaeota Methanocaldococc Methanocaldococc Methanocaldococc Methanocaldococc Methanocaldococc Methanocaldococc Methanocaldococc Methanocaldococc hum Candidatus Nanob Candidatus Candidatus Nanob Candidatus Thermodesulfatato Methanothermoco boonei haeum cryptofilum haeum Methanotorris form Methanotorris ThermodesulfatatoAmmonifex degen boonei faticallidus haeum cryptofilum haeum Methanotorris ign Methanotorris Thermodesulfatato sp. MAR08-339 sp. Methanocaldococc . 128-5-R1-1 haeota archaeon haeota F5 Thermosulfurimon ontis thermarum hypogea Aquifex aeolicus Aquifex PersephonellaPersephonella
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  • Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park

    Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park

    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.
  • A Survey of Carbon Fixation Pathways Through a Quantitative Lens

    A Survey of Carbon Fixation Pathways Through a Quantitative Lens

    Journal of Experimental Botany, Vol. 63, No. 6, pp. 2325–2342, 2012 doi:10.1093/jxb/err417 Advance Access publication 26 December, 2011 REVIEW PAPER A survey of carbon fixation pathways through a quantitative lens Arren Bar-Even, Elad Noor and Ron Milo* Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel * To whom correspondence should be addressed. E-mail: [email protected] Received 15 August 2011; Revised 4 November 2011; Accepted 8 November 2011 Downloaded from Abstract While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it http://jxb.oxfordjournals.org/ has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures at Weizmann Institute of Science on July 3, 2016 of yet unknown carbon fixation pathways are suggested and discussed.