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- なぎさ いちぞの
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13 Summary Evaluation of carbon dioxide fixing ability and development of the usetechnology of carbon dioxide fixing ability by the non-photoautotrophicmicroorganism 1. Objectives of the project This project aims at the probability of the basic technology necessary for construction of high-efficient carbon dioxide fixation system by non-photoautotrophic microorganismand useful compound production system construction from carbon dioxide using carbondioxide fixation gene cluster which the high-efficient non-photoautotrophic carbondioxide fixation microorganism possesses. 2. Content of Enforcement. The existence of chemi-autotrophs which fix the carbon dioxide by the route which does not base on the photosynthesis in the organism is also known, and non-calvine types carbon dioxide fixation route such as the reductive ticarboxylic acid cycle are identified recently. And, it becomes clear that Rubisco in hyper thermophilic archaebacteria such asthermococcus kodakaraensis KOD1 with the high specific activity exists. It is sufficiently expected that high-efficient carbon dioxide fixation system and carbon dioxide fixation enzyme in these non- photoautotrophic microorganisms exist. And, it is also expected that same kinds of usufull product except usual microbial compound. It was noticed in respect of these, and the examination was started on following items. A) An investigation of new non-photoautotrophic microorganism with the CO2 fixation ability. B) Elucidation and evaluation of the CO2fixation mechanism of nonphotoautotrophicmicroorganism with CO2 fixation ability. 3. Result in 2002 Fiscal Year (1) An investigation of new non-photoautotrophic microbe which has CO2 fixing ability. (a) An investigation of new non-photoautotrophic microbe. Separation of a new non-photoautotrophic microbe which has CO2 fixing ability was continued. Cultivation of the non-photoautotrophic microbe at degrees C from 70 samples under various environment were performed. Although growth was not achieved in the culture medium for methane microbe, growth were obtained in the culture medium for Hyper-thermophilic Arhcaebacteria and the culture medium for 3
14 sulfate reducing microbe, and the culture medium for sulfur oxidization microbe. (b) Examination of production of a useful substance. Investigation of biological synthetic pathway of a poly ether lipid which exists in Archaea including a methane microb. The genes which constitutes the biological synthetic pathway of geranylgeranyl di phosphate that is a precursor of the poly ether lipid from mevalonate via isopentenyl di phosphate was existed in a genome of Sulfolobus solfataricus which is a member of hyper-thermophilic archaea. Furthermore, examination was proceeded about a possibility of a high-speed methane generation system configuration under a high temperature condition from an organic waste. Posibility of the high-speed methane generation under low concentration hydrogen and high temperature with a combination of a methane generation from hydrogen and CO2 by the hyper-thermophilic methane microbe and a hydrogen generation from organic waste by the hyper-thermophiles was estimated. (c) Analysis of the key enzymes which constitute a reductive-tca cycle. Eenzyme genes were obtained for the purpose of a functional analysis of phosphoenolpyruvate carboxylase and Oxoglutarate shynthase which constitute the reductive-tca cycle that was estimated its energy efficiency and carbon dioxide fixation efficiency were the highest by investigation in the 2001 fiscal year. (2) The elucidation of the fixing mechanism of a non-photoautotrophic microbe which has CO2 fixing ability (a) Analysis of a genome of Thermococcus kodakaraensis KOD1, CO2 fixation enzymes, and decarboxylation enzyme. Genomic analysis of hyper-thermophilic archaeon Thermococcus kodakaraensis KOD1 was continued. Genes of KOD1 were estimated to be about 2000, and has checked some CO2 fixing enzymes and some enzymes related carbon metabolism in this strain by homology search. Novel gene disruption system of KOD1 by a homologous recombination using a pyrf gene deficient mutant strain as a host has been established. Using the pyrf gene as a selection marker which complement uracil requirement, some mutants which had tolerance for 5-fluoroorotate and which also had uracil requirement were isolated. Functional analysis of enzymes involved in CO2 fixation was carried focused on Rubisco and Formate dehydrogenase. (b) Elucidation and evaluation of the fixation mechanism of non- photoautotrophic microorganism with CO2 fixation ability. () An investigation of new non- photoautotrophic microbe. Separation of a new non- photoautotrophic microbe was tried from the Sagara oil field 4
15 underground digging sample, some strains considered to be a sulfate reducing microbes were separated. (c) The modification of a useful enzyme of KOD1, and a transgenetics of the enzyme gene to other living things. Tk-Rubisco shows very high relative activity under high temperature. A method to change its activity at ambient temperature was developed for the purpose of introducing this Tk-Rubisco into a plant aiming at improvement of CO2 fixing ability. A new screening method to isolate desired mutant Rubisco has been developed, using purple non-sulfur bacteria as a host. 5
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17 (Ralstonia, Hydrogenovibrio ) (Synechococcus, Spirulina ) (Thiobacillus ) (Rhodobacter, Rhodospirillum ) (Nitrosomonas ) (Chromatium ) (Nitrobacter ) ( Methanobacterium ) Acetyl-CoA (Clostridium ) 3-HP (3-hydroxypropionate cycle) (Chloroflexus ) (Acidianus, Sulfolobus ) TCA (Hydrogenobacter ) (Chlorobium ) (RTCA cycle) (Desulfobacter ) 7
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52 modifiedseqence 42
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56 4Clostridium acetobutylicum OXO seqence 46
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59 TCA 49
60 Thermococcus kodakaraensis KOD1 Thermococcus kodakaraensis KOD1 (1) KOD1 16SrRNA DNA PCR DNA DNA (2~4) KOD KOD1 KOD1 T. kodakaraensis KOD1 50
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62 KOD1 bacteria (5, archaea 3 6) 2Mbp Thermococcus kodakaraensis KOD1 Euryarchaeota Thermococcales Thermococcales 3 Pyrococcus P. furiosus, P. abyssi, P. horikoshii Thermococcus Thermococcus T. kodakaraensis KOD1 T. kodakaraensis KOD1 DNA shotgun clone library 2,089,377bp GC 52% Orc1/CDC6 1,000bp AT rich open reading frame (ORF) 2,293 NCBI COGs 43% 41% COGs P. abyssi, P. horikoshii 52
63 KOD1 53
64 amya α-amylase hpka, hpkb histone A and B aspb glutamate synthase hydbgda hydrogenase aspc aspartate aminotransferase hypcd hydrogenase-accessory proteins asps aspartyl-trna synthetase iorab indolepyruvate ferredoxin oxidoreductase cdca cell division control protein lig ATP-dependent DNA ligase cgt cyclodextrin glucanotransferase lon Lon protease chia chitinase malq 4-α-glucanotransferase cobq cobyric acid synthase pol DNA polymerase family B cobs cobalamin 5'-phosphate synthase prsa ribose phosphate pyrophosphokinase cpka, cpkb chaperonin a and b pyrf orotidine-5'-phosphate decarboxylase eno enolase rbc Rubisco fba fructose 1,6-bisphosphate aldolase rnhb RibonucleaseH II fdhabc formate dehydrogenase sub subtilisin-like protease precursor fdx ferredoxin tbp TATA-binding protein flab flagellin B tip49 TBP-interacting protein gdha glutamate dehydrogenase trpcdeghba tryptophan biosynthesis operon glm glucosaminidase trxb thioredoxin reductase glna glutamine synthetase tubb ftsz homologue glpk glycerol kinase yccy tyrosine phosphatase gly β-glycosidase KOD1 ORF map 54
65 KOD1 KOD1 uracil pyrf (orotidylate decarboxylase ) pyrf pyrf fluoroorotic acid (5-FOA) uracil 6 PyrF 2 KU25, KU27 uracil PyrF, PyrE Strain Activity (µmol mg -1 min -1 ) PyrF PyrE KOD1 (WT) KU KU KU KU KU KU pyrf KU25 TA KU27 CG pyrf KU25 Uracil 55
66 KU25 KU27 pyrf KU25 Uracil 56
67 KU25 trpeanthranilate synthase trpe pyrf KU25 uracil KW4 trpe pyrf PCR Southern blot hybridization Southern blot KW4 pyrf 57
68 KW4 Southern blot 58
69 T. kodakaraensis KOD1 (7) DNA 59
70 (1) Morikawa M, Izawa Y, Rashid N, Hoaki T, Imanaka T. Purification and characterization of a thermostable thiol protease from a newly isolated hyperthermophilic Pyrococcus sp. Appl Environ Microbiol Dec;60(12): (2) Nishioka M, Fujiwara S, Takagi M, Imanaka T. Characterization of two intein homing endonucleases encoded in the DNA polymerase gene of Pyrococcus kodakaraensis strain KOD1. Nucleic Acids Res Oct 1;26(19): (3) Hashimoto H, Matsumoto T, Nishioka M, Yuasa T, Takeuchi S, Inoue T, Fujiwara S, Takagi M, Imanaka T, Kai Y. Crystallographic studies on a family B DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1. J Biochem (Tokyo) Jun;125(6):983-6 (4) Hashimoto H, Takahashi H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, Kai Y. Crystallographic study of intein homing endonuclease II encoded in the archaeal DNA polymerase gene. Acta Crystallogr D Biol Crystallogr Sep;56 ( Pt 9): (5) Mankin AS, Kagramanova VK, Teterina NL, Rubtsov PM, Belova EN, Kopylov AM, Baratova LA, Bogdanov AA. The nucleotide sequence of the gene coding for the 16S rrna from the archaebacterium Halobacterium halobium. Gene. 1985;37(1-3): (6) Olsen GJ, Pace NR, Nuell M, Kaine BP, Gupta R, Woese CR. Sequence of the 16S rrna gene from the thermoacidophilic archaebacterium Sulfolobus solfataricus and its evolutionary implications. 60
71 J Mol Evol. 1985;22(4): (7) Sato T, Fukui T, Atomi H, Imanaka T. Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol Jan;185(1):
72 KOD1 Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) KOD1 Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) (1) Rubisco Calvin-Benson-Bassham cyclecbb cycle, Calvin (2~5) Rubisco ribulose 1,5-bisphosphate CO phosphoglycerate (3-PGA) carboxylase Rubisco CO 2 O 2 3-PGA 2-phosphoglycolate (2-PG) oxygenase 62
73 Rubisco oxygenase carboxylase/oxygenase Rubisco 55kDa, 15kDa L 8 S 8 16 Type I 50kDa L 2 Type II type 70% Type I-Type II 50% Rubisco 63
74 KOD1 Rubisco Calvin Tk-Rubisco Type I, Type II Rubisco Archaeoglobus, Methanococcus, Pyrococcus Rubisco 64
75 Tk-Rubisco Rubisco 70µmol CO 2 fixed mg -1 min -1 SpinachRubisco 2µmol CO 2 fixed mg -1 min Tk-Rubisco 65
76 carboxylase Tk-Rubisco Temperature () KOD1 total RNA Northern blot Western blot KOD1 Tk-Rubisco KOD1 native Tk-Rubisco Tk-Rubisco 2.8 Tk-Rubisco X- (6, 7) L 2 dimer 150 pentagonal decamer 66
77 Tk-Rubisco Tk-Rubisco 67
78 L 2 dimer 2 Type I, Type II Tk-Rubisco L 2 dimer Glu63, Arg66, Asp69 Tk-Rubisco 68
79 3 Ser E63S, R66S, D69S 3 E63S/R66S/D69S (8) 30 E63SD69S 10 R66S 10 2 E63S/R66S/D69S 2 E63SD69S D69S Tk-Rubisco 69
80 E63SR66S E63S/R66S/D69S D69S 110 Tk-Rubisco 70
81 Tk-Rubisco KOD1 Rubisco Rubisco DNA 71
82 (1) Ezaki S, Maeda N, Kishimoto T, Atomi H, Imanaka T. Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. J Biol Chem Feb 19;274(8): (2) Ryan FJ, Tolbert NE. Ribulose diphosphate carboxylase/oxygenase. III. Isolation and properties. J Biol Chem Jun 10;250(11): (3) Read BA, Tabita FR. High substrate specificity factor ribulose bisphosphate carboxylase/oxygenase from eukaryotic marine algae and properties of recombinant cyanobacterial RubiSCO containing "algal" residue modifications. Arch Biochem Biophys Jul;312(1): (4) Steinberg NA, Meeks JC. Photosynthetic CO 2 fixation and ribulose bisphosphate carboxylase/oxygenase activity of Nostoc sp. strain UCD 7801 in symbiotic association with Anthoceros punctatus. J Bacteriol Nov;171(11): (5) Hirota R, Kato J, Morita H, Kuroda A, Ikeda T, Takiguchi N, Ohtake H. Related Articles, Links Isolation and characterization of cbbl and cbbs genes encoding form I ribulose-1,5-bisphosphate carboxylase/oxygenase large and small subunits in Nitrosomonas sp. strain ENI-11. Biosci Biotechnol Biochem Mar;66(3): (6) Maeda N, Kitano K, Fukui T, Ezaki S, Atomi H, Miki K, Imanaka T. Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a 72
83 pentagonal structure. J Mol Biol Oct 15;293(1): (7) Kitano K, Maeda N, Fukui T, Atomi H, Imanaka T, Miki K. Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry. Structure (Camb) Jun;9(6): (8) Maeda N, Kanai T, Atomi H, Imanaka T. The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability. J Biol Chem Aug 30;277(35):
84 KOD1 Formate oxidoreductasefor FOR FOR 1 NAD + (1) 1 (2~4) 1 KOD1 FOR FOR 74
85 FOR KOD1FOR 4 ORF (Tk-for ABCD) Tk-ForA Tk-ForBC Tk-ForD FOR KOD1 Thermococcus Pyrococcus FOR KOD1 FOR KOD1 FOR 75
86 FOR FOR FDH Mo W FOR 76
87 FOR U/mg 0.5%YE+0.5%triptone Mo (10 µm) W (10 µm) Mo + W 10 µm 8.5 KOD1 FOR KOD1 FOR Tk-for Tk-ForA Tk-ForA Tk-ForA FOR KOD1 Tk-For FOR SDS-PAGE N- Western blot Tk-For ForA, ForB ForC Tk-For ForA, ForB 2 Tk-For
88 ph min70 1 methyl viologen, benzyl viologen NAD +, NADP +, FAD +, FMN + For Methyl viologen 100 Benzyl viologen 185 FAD 3 FMN 8 NAD + 8 NADP + 5 ForA FOR Tk-ForAB 1 mol 11.9 mol 15.5 mol 3, 4 78
89 Tk-FOR mol/for AB Mo < 0.01 W 0.6 Fe 11.9 S 15.5 Tk-FOR 79
90 (1) Overkamp KM, Kotter P, van der Hoek R, Schoondermark-Stolk S, Luttik MA, van Dijken JP, Pronk JT. Functional analysis of structural genes for NAD(+)-dependent formate dehydrogenase in Saccharomyces cerevisiae. Yeast Apr;19(6): (2) Laukel M, Chistoserdova L, Lidstrom ME, Vorholt JA. The tungsten-containing formate dehydrogenase from Methylobacterium extorquens AM1: purification and properties. Eur J Biochem Jan;270(2): (3) Boyington JC, Gladyshev VN, Khangulov SV, Stadtman TC, Sun PD. Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster. Science Feb 28;275(5304): (4) Ferry JG. Formate dehydrogenase. FEMS Microbiol Rev Dec;7(3-4):
91 HD-1 (1, 2) HD-1 PHA (polyhydroxyalkanoate) HD-1 81
92 16SrRNA Proteobacteria 82
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94 M4, ON CO µm 1% (w/v) % (w/v) 2 2 M4 ON M4 ON Na 2 HPO 4 6 g (NH 4 ) 2 SO 4 2 g KH 2 PO 4 3 g MgSO g NH 4 Cl 1 g CaCl g NaCl 0.5 g FeSO 4 10 mg CaCl 2 3 mg KH 2 PO 4 4 g MgSO mg DW Up to 1000ml DW Up to 1000ml 16 16SrRNA 16 Pseudomonas stutzeri P. stutzeri (3) CO 2 84
95 2 Fe 3+ 85
96 No. M9 ON
97 (1) Morikawa M., Imanaka T. Isolation of a new mixotorophic bacterium which can fix CO 2 and assimilate alihatic and aromatic-hydrocarbons anaerobically. J. Ferment. Bioenginer (4): (2) Kanamori T, Rashid N, Morikawa M, Atomi H, Imanaka T. Oleomonas sagaranensis gen. nov., sp. nov., represents a novel genus in the alpha-proteobacteria. FEMS Microbiol Lett Dec 17;217(2): (3) Sorokin DY, Teske A, Robertson LA, Kuenen JG. Anaerobic oxidation of thiosulfate to tetrathionate by obligately heterotrophic bacteria, belonging to the Pseudomonas stutzeri group. FEMS Microbiol Ecol Oct 1;30(2):
98 KOD1 KOD1 Rubisco (Tk-Rubisco) T. kodakaraensis KOD1 Calvin Rubisco Rubisco Tk-Rubisco L 8 S 8 Rubisco Tk-Rubisco Rubisco Rubisco Rubisco Rubisco (1~4) Rubisco Rubisco Tk-Rubisco Type-I Rubisco Rubisco Rubisco (5) KOD1 Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) Rubisco Calvin Rubisco 88
99 RITE Rhodopseudomonas palustris No.7 Rubisco (6) pmg103/pmg105 (7) ApaLI XhoI EcoRI SacI KpnI BamHI XbaI SalI Sse8387I SphI lacz Km r phsg298 ori pmg10 3 5,680 bp pmg101 ori ClaI (XhoI/SalI) Inui M. et al. Appl. Environ. Microbiol., 66:54-63 pmg105 pmg103 pmg103 89
100 phosphoenolpyruvate carboxykinase (PEPCK) promoter (8) Tk-Rubisco R. palustris No.7 R. palustris No.7 PEPCK promoter DNA 2 PCR PEPCK promoter EcoRI, SalI PEPCK promoter puc118 R. palustris genome DNA PEPCK promoter RBS PEPCK ORF Rpckp-f 1 Rpck-r kb pckp-ec o EcoRI 0.2 kb BamHI-NdeI-SalI pckp-sn B PEPCK 90
101 Rpckp-f1 : 5 -CGGAATGACTTGAGCCAGCG-3 Rpck-r1 : 5 -CCAGCCGGTGTTGACCAGCC-3 R. palustris No.7 PEPCK ORF DNA PCR 1.5 kbp pckp-eco : 5 -GGCGGTAAACGAATTCATGCCGGCCGGGTTGGC-3 EcoRI site pckp-snb : 5 -CCGTTATGGTCGACCGTCTCTTGCATATGTGGATCCTCCTCG-3 SalI, NdeI, BamHI site PEPCK ORF PEPCK PEPCK pet21a Tk-Rubisco NdeI, SalI 91
102 puc118pckpes pucpckprbc DH5α 92
103 pucpckprbc EcoRI 4.65 kbp EcoRI, BamHI PEPCK 0.2 kbp EcoRI, BamHI, SalI Tk-rbc pucpckprbc puc118 93
104 PCR EcoRI, SalI E. coli R. palustris pmg103 EcoRI, SalI Tk-Rubisco pm3rbcwt 94
105 pm3rbcwt E. coli DH5α LB PCR 1.5 kbp DNA R. palustris PEPCK promoter RP Tk-Rubisco N TNC TC PCR PCR pm3rbcwt A TN TC PCR B RP TC PCR 95
106 R. palustris No.7 Tk-Rubisco pm3rbcwt R. palustris No.7 pm3rbcwt OD µl Milli-Q 10% 100µl 10% A A40µl pm3rbcwt 1µl 0.2cm gap cuvette Gene pulse 200, 2.5kV, 25µF 1ml SOC µl SOC 200µM Km x 10 3 cells /µg DNA R. palustris PEPCK promoter RP Tk-Rubisco N TN C TC PCR PCR R. palustris Tk-Rubisco 96
107 pm3rbcwt R. palustris A TN TC PCR B RP TC PCR 2003 Tk-Rubisco Rubisco R. palustris 97
108 Tk-Rubisco 98
109 (1) Delwiche CF, Palmer JD. Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol Biol Evol Jul;13(6): (2) Hwang SR, Tabita FR. Cotranscription, deduced primary structure, and expression of the chloroplast-encoded rbcl and rbcs genes of the marine diatom Cylindrotheca sp. strain N1. J Biol Chem Apr 5;266(10): (3) Kanevski I, Maliga P, Rhoades DF, Gutteridge S. Plastome engineering of ribulose-1,5-bisphosphate carboxylase/oxygenase in tobacco to form a sunflower large subunit and tobacco small subunit hybrid. Plant Physiol Jan;119(1): (4) Reith ME, Cattolico RA. In vivo chloroplast protein synthesis by the chromophytic alga Olisthodiscus luteus. Biochemistry May 7;24(10): (5) Maeda N, Kanai T, Atomi H, Imanaka T. Related Articles, Links The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability. J Biol Chem Aug 30;277(35): (6) Inui M Yukawa H et al. unpublished data (7) Inui M, Roh JH, Zahn K, Yukawa H. Sequence analysis of the cryptic plasmid pmg101 from Rhodopseudomonas palustris and construction of stable cloning vectors. 99
110 Appl Environ Microbiol Jan;66(1): (8) Inui M, Nakata K, Roh JH, Zahn K, Yukawa H. Related Articles, Links Molecular and functional characterization of the Rhodopseudomonas palustris no. 7 phosphoenolpyruvate carboxykinase gene. J Bacteriol May;181(9):
111 TCA Thermococcus kodakaraensis KOD1 RuBisCO 14 CO2 CO2
112 CO2 CO Sulfolobussolfataricus CO2 CO2
113 CO CO2 Tk-rbc Rubisco Tk-rbc Tk-rbc Tk-rbc Tk-rbc PCR CO2 Rubisco Rubisco 2 55 CO2 70
114 CO2 Tk-rbc Tk-rbc Tk-rbc Rubisco Rubisco Tk-rbc Tk-rbc Tk-rbc Tk-rbc PCR CO2 Rubisco Rubisco
115 Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 J Bacteriol Jan;185(1): Sato T., Fukui T., Atomi H., Imanaka T. Oleomonas sagaranensis gen. nov., sp. nov., represents a novel genus in the alpha-proteobacteria. FEMS Microbiol Lett Dec 17;217(2): Kanamori T., Rashid N., Morikawa T., Atomi H., Imanaka T. The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability. J Biol Chem Aug 30;277(35): Maeda N., Kanai T., Atomi H., Imanaka T. The 4th international congress on extremophiles 2002, Sep., Naples, Italy Complete genome analysis of the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1 Imanaka T., Fukui T., Kanai T., Fujiwara S., Atomi H. The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability. Atomi H., Maeda N., Kanai T., Imanak T Thermococcus kodakaraensis KOD1 Thermococcus kodakaraensis KOD1 105
116 Thermococcus kodakaraensis KOD1 HD-1 Thermococcus kodakaraensis KOD1 Thermococcus kodakaraensis KOD1 106
117 (RITE)
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