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Distinct modified nucleosides in tRNATrp from the hyperthermophilic archaeon Thermococcus kodakarensis and requirement of tRNA m2G10/m2 2G10 methyltransferase (archaeal Trm11) for survival at high temperatures.

Hirata A, Suzuki T, Nagano T, Fujii D, Okamoto M, Sora M, Lowe TM, Kanai T, Atomi H, Suzuki T, Hori H.

J Bacteriol. 2019 Aug 12. pii: JB.00448-19. doi: 10.1128/JB.00448-19. [Epub ahead of print]


Identification of Dephospho-Coenzyme A (Dephospho-CoA) Kinase in Thermococcus kodakarensis and Elucidation of the Entire CoA Biosynthesis Pathway in Archaea.

Shimosaka T, Makarova KS, Koonin EV, Atomi H.

MBio. 2019 Jul 23;10(4). pii: e01146-19. doi: 10.1128/mBio.01146-19.


Branched-chain polyamine stabilizes RNA polymerase at elevated temperatures in hyperthermophiles.

Yamori Y, Hamakawa M, Hidese R, Fukuda M, Atomi H, Fukuda W, Fujiwara S.

Amino Acids. 2019 May 17. doi: 10.1007/s00726-019-02745-y. [Epub ahead of print]


Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA.

Kwon S, Watanabe S, Nishitani Y, Kawashima T, Kanai T, Atomi H, Miki K.

Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):7045-7050. doi: 10.1073/pnas.1801955115. Epub 2018 Jun 18.


A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate.

Aziz I, Bibi T, Rashid N, Aono R, Atomi H, Akhtar M.

J Bacteriol. 2018 Jul 25;200(16). pii: e00284-18. doi: 10.1128/JB.00284-18. Print 2018 Aug 15.


Crystal structures of an archaeal chitinase ChiD and its ligand complexes.

Nishitani Y, Horiuchi A, Aslam M, Kanai T, Atomi H, Miki K.

Glycobiology. 2018 Jun 1;28(6):418-426. doi: 10.1093/glycob/cwy024.


Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants.

Nagata R, Fujihashi M, Sato T, Atomi H, Miki K.

Nat Commun. 2018 May 2;9(1):1765. doi: 10.1038/s41467-018-04201-z.


Hyperthermophilic Archaeon Thermococcus kodakarensis Utilizes a Four-Step Pathway for NAD+ Salvage through Nicotinamide Deamination.

Hachisuka SI, Sato T, Atomi H.

J Bacteriol. 2018 May 9;200(11). pii: e00785-17. doi: 10.1128/JB.00785-17. Print 2018 Jun 1.


Structure of a [NiFe] hydrogenase maturation protease HycI provides insights into its substrate selectivity.

Kwon S, Nishitani Y, Hirao Y, Kanai T, Atomi H, Miki K.

Biochem Biophys Res Commun. 2018 Apr 15;498(4):782-788. doi: 10.1016/j.bbrc.2018.03.058. Epub 2018 Mar 15.


A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile.

Nunoura T, Chikaraishi Y, Izaki R, Suwa T, Sato T, Harada T, Mori K, Kato Y, Miyazaki M, Shimamura S, Yanagawa K, Shuto A, Ohkouchi N, Fujita N, Takaki Y, Atomi H, Takai K.

Science. 2018 Feb 2;359(6375):559-563. doi: 10.1126/science.aao3407. Epub 2018 Feb 1.


An ornithine ω-aminotransferase required for growth in the absence of exogenous proline in the archaeon Thermococcus kodakarensis.

Zheng RC, Hachisuka SI, Tomita H, Imanaka T, Zheng YG, Nishiyama M, Atomi H.

J Biol Chem. 2018 Mar 9;293(10):3625-3636. doi: 10.1074/jbc.RA117.001222. Epub 2018 Jan 19.


Phytoene production utilizing the isoprenoid biosynthesis capacity of Thermococcus kodakarensis.

Fuke T, Sato T, Jha S, Tansengco ML, Atomi H.

Extremophiles. 2018 Mar;22(2):301-313. doi: 10.1007/s00792-018-0998-7. Epub 2018 Jan 16.


Possible function of the second RecJ-like protein in stalled replication fork repair by interacting with Hef.

Nagata M, Ishino S, Yamagami T, Simons JR, Kanai T, Atomi H, Ishino Y.

Sci Rep. 2017 Dec 5;7(1):16949. doi: 10.1038/s41598-017-17306-0.


Identification of the glucosamine kinase in the chitinolytic pathway of Thermococcus kodakarensis.

Aslam M, Takahashi N, Matsubara K, Imanaka T, Kanai T, Atomi H.

J Biosci Bioeng. 2018 Mar;125(3):320-326. doi: 10.1016/j.jbiosc.2017.10.005. Epub 2017 Nov 14.


An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus.

Ikeda Y, Okada Y, Sato A, Kanai T, Tomita M, Atomi H, Kanai A.

Sci Rep. 2017 Oct 4;7(1):12674. doi: 10.1038/s41598-017-13062-3.


The Cdc45/RecJ-like protein forms a complex with GINS and MCM, and is important for DNA replication in Thermococcus kodakarensis.

Nagata M, Ishino S, Yamagami T, Ogino H, Simons JR, Kanai T, Atomi H, Ishino Y.

Nucleic Acids Res. 2017 Oct 13;45(18):10693-10705. doi: 10.1093/nar/gkx740.


Gene regulation of two ferredoxin:NADP+ oxidoreductases by the redox-responsive regulator SurR in Thermococcus kodakarensis.

Hidese R, Yamashita K, Kawazuma K, Kanai T, Atomi H, Imanaka T, Fujiwara S.

Extremophiles. 2017 Sep;21(5):903-917. doi: 10.1007/s00792-017-0952-0. Epub 2017 Jul 7.


Metabolism Dealing with Thermal Degradation of NAD+ in the Hyperthermophilic Archaeon Thermococcus kodakarensis.

Hachisuka SI, Sato T, Atomi H.

J Bacteriol. 2017 Sep 5;199(19). pii: e00162-17. doi: 10.1128/JB.00162-17. Print 2017 Oct 1.


An In Vitro Enzyme System for the Production of myo-Inositol from Starch.

Fujisawa T, Fujinaga S, Atomi H.

Appl Environ Microbiol. 2017 Aug 1;83(16). pii: e00550-17. doi: 10.1128/AEM.00550-17. Print 2017 Aug 15.


Engineering of the Hyperthermophilic Archaeon Thermococcus kodakarensis for Chitin-Dependent Hydrogen Production.

Aslam M, Horiuchi A, Simons JR, Jha S, Yamada M, Odani T, Fujimoto R, Yamamoto Y, Gunji R, Imanaka T, Kanai T, Atomi H.

Appl Environ Microbiol. 2017 Jul 17;83(15). pii: e00280-17. doi: 10.1128/AEM.00280-17. Print 2017 Aug 1.


Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis.

Nagata R, Fujihashi M, Kawamura H, Sato T, Fujita T, Atomi H, Miki K.

ACS Chem Biol. 2017 Jun 16;12(6):1514-1523. doi: 10.1021/acschembio.7b00064. Epub 2017 Apr 18.


An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism.

Makino Y, Sato T, Kawamura H, Hachisuka SI, Takeno R, Imanaka T, Atomi H.

Nat Commun. 2016 Nov 18;7:13446. doi: 10.1038/ncomms13446.


Structure and function of an ancestral-type β-decarboxylating dehydrogenase from Thermococcus kodakarensis.

Shimizu T, Yin L, Yoshida A, Yokooji Y, Hachisuka SI, Sato T, Tomita T, Nishida H, Atomi H, Kuzuyama T, Nishiyama M.

Biochem J. 2017 Jan 1;474(1):105-122. doi: 10.1042/BCJ20160699. Epub 2016 Nov 9.


Genetic analyses of the functions of [NiFe]-hydrogenase maturation endopeptidases in the hyperthermophilic archaeon Thermococcus kodakarensis.

Kanai T, Yasukochi A, Simons JR, Scott JW, Fukuda W, Imanaka T, Atomi H.

Extremophiles. 2017 Jan;21(1):27-39. doi: 10.1007/s00792-016-0875-1. Epub 2016 Oct 13.


Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.

Yoshida A, Tomita T, Atomi H, Kuzuyama T, Nishiyama M.

J Biol Chem. 2016 Oct 7;291(41):21630-21643. Epub 2016 Aug 26.


Crystal structure of the TK2203 protein from Thermococcus kodakarensis, a putative extradiol dioxygenase.

Nishitani Y, Simons JR, Kanai T, Atomi H, Miki K.

Acta Crystallogr F Struct Biol Commun. 2016 Jun;72(Pt 6):427-33. doi: 10.1107/S2053230X16006920. Epub 2016 May 23.


Mutation design of a thermophilic Rubisco based on three-dimensional structure enhances its activity at ambient temperature.

Fujihashi M, Nishitani Y, Kiriyama T, Aono R, Sato T, Takai T, Tagashira K, Fukuda W, Atomi H, Imanaka T, Miki K.

Proteins. 2016 Oct;84(10):1339-46. doi: 10.1002/prot.25080. Epub 2016 Jun 24.


Crystal structure of a [NiFe] hydrogenase maturation protease HybD from Thermococcus kodakarensis KOD1.

Kwon S, Nishitani Y, Watanabe S, Hirao Y, Imanaka T, Kanai T, Atomi H, Miki K.

Proteins. 2016 Sep;84(9):1321-7. doi: 10.1002/prot.25070. Epub 2016 Jun 8.


Regulation of Coenzyme A Biosynthesis in the Hyperthermophilic Bacterium Thermotoga maritima.

Shimosaka T, Tomita H, Atomi H.

J Bacteriol. 2016 Jun 27;198(14):1993-2000. doi: 10.1128/JB.00077-16. Print 2016 Jul 15.


Crystal structure of ketopantoate reductase from Thermococcus kodakarensis complexed with NADP(.).

Aikawa Y, Nishitani Y, Tomita H, Atomi H, Miki K.

Acta Crystallogr F Struct Biol Commun. 2016 May;72(Pt 5):369-75. doi: 10.1107/S2053230X16005033. Epub 2016 Apr 22.


A Structurally Novel Chitinase from the Chitin-Degrading Hyperthermophilic Archaeon Thermococcus chitonophagus.

Horiuchi A, Aslam M, Kanai T, Atomi H.

Appl Environ Microbiol. 2016 May 31;82(12):3554-3562. doi: 10.1128/AEM.00319-16. Print 2016 Jun 15.


Crystal structures of chitin binding domains of chitinase from Thermococcus kodakarensis KOD1.

Hanazono Y, Takeda K, Niwa S, Hibi M, Takahashi N, Kanai T, Atomi H, Miki K.

FEBS Lett. 2016 Jan;590(2):298-304. doi: 10.1002/1873-3468.12055. Epub 2016 Jan 20.


Crystal structure of archaeal ketopantoate reductase complexed with coenzyme a and 2-oxopantoate provides structural insights into feedback regulation.

Aikawa Y, Nishitani Y, Tomita H, Atomi H, Miki K.

Proteins. 2016 Mar;84(3):374-82. doi: 10.1002/prot.24984. Epub 2016 Feb 3.


Overproduction of the membrane-bound [NiFe]-hydrogenase in Thermococcus kodakarensis and its effect on hydrogen production.

Kanai T, Simons JR, Tsukamoto R, Nakajima A, Omori Y, Matsuoka R, Beppu H, Imanaka T, Atomi H.

Front Microbiol. 2015 Aug 26;6:847. doi: 10.3389/fmicb.2015.00847. eCollection 2015.


Sodium-driven energy conversion for flagellar rotation of the earliest divergent hyperthermophilic bacterium.

Takekawa N, Nishiyama M, Kaneseki T, Kanai T, Atomi H, Kojima S, Homma M.

Sci Rep. 2015 Aug 5;5:12711. doi: 10.1038/srep12711.


Editorial overview: Extremophiles: From extreme environments to highly stable biocatalysts.

Bonch-Osmolovskaya E, Atomi H.

Curr Opin Microbiol. 2015 Jun;25:vii-viii. doi: 10.1016/j.mib.2015.06.005. Epub 2015 Jun 23. No abstract available.


Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer.

Watanabe S, Kawashima T, Nishitani Y, Kanai T, Wada T, Inaba K, Atomi H, Imanaka T, Miki K.

Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):7701-6. doi: 10.1073/pnas.1503102112. Epub 2015 Jun 8.


Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation.

Nagata R, Fujihashi M, Sato T, Atomi H, Miki K.

Biochemistry. 2015 Jun 9;54(22):3494-503. doi: 10.1021/acs.biochem.5b00296. Epub 2015 May 29.


A pentose bisphosphate pathway for nucleoside degradation in Archaea.

Aono R, Sato T, Imanaka T, Atomi H.

Nat Chem Biol. 2015 May;11(5):355-60. doi: 10.1038/nchembio.1786. Epub 2015 Mar 30.


Characterization of a thermostable glucose dehydrogenase with strict substrate specificity from a hyperthermophilic archaeon Thermoproteus sp. GDH-1.

Aiba H, Nishiya Y, Azuma M, Yokooji Y, Atomi H, Imanaka T.

Biosci Biotechnol Biochem. 2015;79(7):1094-102. doi: 10.1080/09168451.2015.1018120. Epub 2015 Mar 9.


International conference on extremophiles 2014.

Antranikian G, Bonch-Osmolovskaya E, Atomi H, Oren A, Adams MW, Santos H.

Extremophiles. 2014 Sep;18(5):789-90. doi: 10.1007/s00792-014-0690-5. No abstract available.


The tryptophan synthase β-subunit paralogs TrpB1 and TrpB2 in Thermococcus kodakarensis are both involved in tryptophan biosynthesis and indole salvage.

Hiyama T, Sato T, Imanaka T, Atomi H.

FEBS J. 2014 Jul;281(14):3113-25. doi: 10.1111/febs.12845. Epub 2014 Jun 10.


Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from Antarctic white rock.

Fukuda W, Chino Y, Araki S, Kondo Y, Imanaka H, Kanai T, Atomi H, Imanaka T.

Int J Syst Evol Microbiol. 2014 Jun;64(Pt 6):2034-40. doi: 10.1099/ijs.0.050005-0. Epub 2014 Mar 20.


Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis.

Kishimoto A, Kita A, Ishibashi T, Tomita H, Yokooji Y, Imanaka T, Atomi H, Miki K.

Proteins. 2014 Sep;82(9):1924-36. doi: 10.1002/prot.24546. Epub 2014 Apr 16.


Different roles of two transcription factor B proteins in the hyperthermophilic archaeon Thermococcus kodakarensis.

Hidese R, Nishikawa R, Gao L, Katano M, Imai T, Kato S, Kanai T, Atomi H, Imanaka T, Fujiwara S.

Extremophiles. 2014 May;18(3):573-88. doi: 10.1007/s00792-014-0638-9. Epub 2014 Mar 14.


An archaeal glutamate decarboxylase homolog functions as an aspartate decarboxylase and is involved in β-alanine and coenzyme A biosynthesis.

Tomita H, Yokooji Y, Ishibashi T, Imanaka T, Atomi H.

J Bacteriol. 2014 Mar;196(6):1222-30. doi: 10.1128/JB.01327-13. Epub 2014 Jan 10.


Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation.

Tominaga T, Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20485-90. doi: 10.1073/pnas.1313620110. Epub 2013 Dec 2.


Characterization of two members among the five ADP-forming acyl coenzyme A (Acyl-CoA) synthetases reveals the presence of a 2-(Imidazol-4-yl)acetyl-CoA synthetase in Thermococcus kodakarensis.

Awano T, Wilming A, Tomita H, Yokooji Y, Fukui T, Imanaka T, Atomi H.

J Bacteriol. 2014 Jan;196(1):140-7. doi: 10.1128/JB.00877-13. Epub 2013 Oct 25.


Identification and characterization of an archaeal ketopantoate reductase and its involvement in regulation of coenzyme A biosynthesis.

Tomita H, Imanaka T, Atomi H.

Mol Microbiol. 2013 Oct;90(2):307-21. doi: 10.1111/mmi.12363. Epub 2013 Aug 27.


An alternative beads-on-a-string chromatin architecture in Thermococcus kodakarensis.

Maruyama H, Harwood JC, Moore KM, Paszkiewicz K, Durley SC, Fukushima H, Atomi H, Takeyasu K, Kent NA.

EMBO Rep. 2013 Aug;14(8):711-7. doi: 10.1038/embor.2013.94. Epub 2013 Jul 9.

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