An Overview of 25 years of Research on Thermococcus Kodakarensis, a Genetically Versatile Model Organism for Archaeal Research

Overview

Journal Folia Microbiol (Praha)

Publisher Springer

Specialty Microbiology

Date 2019 Jul 10

PMID 31286382

Citations 2

Authors

Naeem Rashid

Mehwish Aslam

Affiliations

Soon will be listed here.

Abstract

Almost 25 years have passed since the discovery of a planktonic, heterotrophic, hyperthermophilic archaeon named Thermococcus kodakarensis KOD1, previously known as Pyrococcus sp. KOD1, by Imanaka and coworkers. T. kodakarensis is one of the most studied archaeon in terms of metabolic pathways, available genomic resources, established genetic engineering techniques, reporter constructs, in vitro transcription/translation machinery, and gene expression/gene knockout systems. In addition to all these, ease of growth using various carbon sources makes it a facile archaeal model organism. Here, in this review, an attempt is made to reflect what we have learnt from this hyperthermophilic archaeon.

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References

Santangelo T, Cubonova L, Skinner K, Reeve J . Archaeal intrinsic transcription termination in vivo. J Bacteriol. 2009; 191(22):7102-8. PMC: 2772485. DOI: 10.1128/JB.00982-09. View

Kwon S, Nishitani Y, Watanabe S, Hirao Y, Imanaka T, Kanai T . Crystal structure of a [NiFe] hydrogenase maturation protease HybD from Thermococcus kodakarensis KOD1. Proteins. 2016; 84(9):1321-7. DOI: 10.1002/prot.25070. View

Ladner J, Pan M, Hurwitz J, Kelman Z . Crystal structures of two active proliferating cell nuclear antigens (PCNAs) encoded by Thermococcus kodakaraensis. Proc Natl Acad Sci U S A. 2011; 108(7):2711-6. PMC: 3041083. DOI: 10.1073/pnas.1019179108. View

Akiba T, Ishii N, Rashid N, Morikawa M, Imanaka T, Harata K . Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly. Nucleic Acids Res. 2005; 33(10):3412-23. PMC: 1150280. DOI: 10.1093/nar/gki662. View

Sato T, Fukui T, Atomi H, Imanaka T . Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol. 2002; 185(1):210-20. PMC: 141832. DOI: 10.1128/JB.185.1.210-220.2003. View

Takagi M, Nishioka M, Kakihara H, Kitabayashi M, Inoue H, Kawakami B . Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR. Appl Environ Microbiol. 1997; 63(11):4504-10. PMC: 168769. DOI: 10.1128/aem.63.11.4504-4510.1997. View

Jun S, Hirata A, Kanai T, Santangelo T, Imanaka T, Murakami K . The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration. Nat Commun. 2014; 5:5132. PMC: 4657547. DOI: 10.1038/ncomms6132. View

Fuke T, Sato T, Jha S, Tansengco M, Atomi H . Phytoene production utilizing the isoprenoid biosynthesis capacity of Thermococcus kodakarensis. Extremophiles. 2018; 22(2):301-313. DOI: 10.1007/s00792-018-0998-7. View

Santos C, Tonoli C, Trindade D, Betzel C, Takata H, Kuriki T . Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Proteins. 2010; 79(2):547-57. DOI: 10.1002/prot.22902. View

10.

Takano K, Katagiri Y, Mukaiyama A, Chon H, Matsumura H, Koga Y . Conformational contagion in a protein: structural properties of a chameleon sequence. Proteins. 2007; 68(3):617-25. DOI: 10.1002/prot.21451. View

11.

Bridger S, Lancaster W, Poole 2nd F, Schut G, Adams M . Genome sequencing of a genetically tractable Pyrococcus furiosus strain reveals a highly dynamic genome. J Bacteriol. 2012; 194(15):4097-106. PMC: 3416535. DOI: 10.1128/JB.00439-12. View

12.

Nagata R, Fujihashi M, Kawamura H, Sato T, Fujita T, Atomi H . Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis. ACS Chem Biol. 2017; 12(6):1514-1523. DOI: 10.1021/acschembio.7b00064. View

13.

Watanabe S, Matsumi R, Arai T, Atomi H, Imanaka T, Miki K . Crystal structures of [NiFe] hydrogenase maturation proteins HypC, HypD, and HypE: insights into cyanation reaction by thiol redox signaling. Mol Cell. 2007; 27(1):29-40. DOI: 10.1016/j.molcel.2007.05.039. View

14.

Liman G, Hulko T, Febvre H, Brachfeld A, Santangelo T . A linear pathway for mevalonate production supports growth of Thermococcus kodakarensis. Extremophiles. 2019; 23(2):229-238. DOI: 10.1007/s00792-019-01076-w. View

15.

Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama K, Mayanagi K . Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease. Structure. 2016; 24(11):1960-1971. DOI: 10.1016/j.str.2016.09.005. View

16.

Schlesier J, Siegrist J, Gerhardt S, Erb A, Blaesi S, Richter M . Structural and functional characterisation of the methionine adenosyltransferase from Thermococcus kodakarensis. BMC Struct Biol. 2013; 13:22. PMC: 3853416. DOI: 10.1186/1472-6807-13-22. View

17.

Tanaka S, Matsumura H, Koga Y, Takano K, Kanaya S . Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation. J Mol Biol. 2007; 372(4):1055-1069. DOI: 10.1016/j.jmb.2007.07.027. View

18.

Hashimoto H, Inoue T, Nishioka M, Fujiwara S, Takagi M, Imanaka T . Hyperthermostable protein structure maintained by intra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase. J Mol Biol. 1999; 292(3):707-16. DOI: 10.1006/jmbi.1999.3100. View

19.

Nagata R, Fujihashi M, Sato T, Atomi H, Miki K . Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation. Biochemistry. 2015; 54(22):3494-503. DOI: 10.1021/acs.biochem.5b00296. View

20.

Hirata A, Nishiyama S, Tamura T, Yamauchi A, Hori H . Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules. Nucleic Acids Res. 2016; 44(13):6377-90. PMC: 5291279. DOI: 10.1093/nar/gkw561. View