REVIEW An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research Naeem Rashid 1 & Mehwish Aslam 1 Received: 12 January 2019 /Accepted: 17 June 2019 # Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2019 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. Introduction Thermococcus kodakarensis thrives in a medium augmented with peptides, chitin, starch, or pyruvate, using sulfur or hy- drogen as terminal electron acceptor. It grows rapidly with a doubling time of ∼ 40 min and makes defined colonies on solidified growth medium within 24 h (Atomi et al. 2004a; Morikawa et al. 1994; Nishio et al. 2018). It possesses a small genome of approximately 2 Mbp (Fukui et al. 2005). Soon after the discovery, and much before determination of the complete genome sequence, T. kodakarensis has become one of the best studied hyperthermophilic archaea. Although morphologically and genetically similar to bac- teria (Fig. 1), it shares several characteristics in common with eukaryotes, including the genes encoding proteins involved in transcription and replication (Kim et al. 2003; Nishioka et al. 1998; Nishioka et al. 2001; Rashid et al. 1996; Yamamoto et al. 2006). Some of these proteins, including aspartyl- tRNA synthetase, DNA polymerase D, and RNA polymerase (Fujiwara et al. 1996; Li et al. 2013), are proposed prototypes of their eukaryotic counterparts (Rashid et al. 1995; Rashid et al. 1996). A few proteins from this archaeon are chimeric in structure and possess eukaryotic as well as bacterial features (Imanaka et al. 2006; Imanaka et al. 1995; Schmitt et al. 1998). Culturing ease and high growth rate make T. kodakarensis a facile archaeal model organism which provoked the re- searchers to examine its proteins and metabolic pathways in detail. In this article, we would like to share what T. kodakarensis has taught us. Thermal stability T. kodakarensis grows between 60 and 102 °C, optimal tem- perature at 85 °C (Atomi et al. 2004a). Its DNA and RNA are safeguarded from thermal denaturation by strategies specific for hyperthermophiles. Extreme environmental conditions, in- cluding temperature, pH, and salt, induce stress genes leading to production of stress proteins and molecular chaperones that protect DNA as well as housekeeping cellular machinery (Jia et al. 2015; Lee et al. 2015). Four prefoldin genes are present in this organism whose products keep cellular proteins in na- tive fold during harsh conditions (Danno et al. 2008). T. kodakarensis contains two histones, HpkA and HpkB, to cope with the harsh conditions. It has been shown that HpkB possessed higher ability to prevent double-stranded DNA from thermal denaturation than HpkA in vitro (Higashibata et al. 1999). In addition to these, T. kodakarensis contains two chaperonins, CpkA and CpkB, involved in protein pro- tection. Their encoding genes are expressed in temperature- and growth phase-dependent fashion. It has been shown that CpkA is necessary for cell growth at 60 °C and CpkB at 93 °C (Fujiwara et al. 2008). Similarly, polyamines are known to * Naeem Rashid naeem.ff.sbs@pu.edu.pk; naeemrashid37@hotmail.com 1 School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan Folia Microbiologica https://doi.org/10.1007/s12223-019-00730-2