Microbe Profile: Thermococcus kodakarensis: the model hyperthermophilic archaeon

Abstract

Thermococcus kodakarensis cells are polyploid and genome duplication does not require an origin of replication. Secreted enzymes depolymerize starch into malto-oligosaccharides (Glu) n and chitin into N-,N-diacetylchitobiose (GlcNAc) 2 , which serve as substrates for growth and hydrogen production. Combining genetics and biochemistry revealed previously unknown metabolic pathways, a novel role for RuBisCO and distinct roles for the three ferredoxins (Fds). The electron micrograph was taken by Dr Tomoya Imai (Kyoto University).

Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis

“…With histone composition altered in strain TS622, and histone-composition and extended AHCP formation disrupted in strain TS620, we sought to quantify the transcriptomes of each strain in response to an environmental shift ( Jäger et al, 2014 ; Atomi and Reeve, 2019 ). Environmentally cued changes to histone-based chromatin architecture are a known mechanism to regulate gene expression, and for the Thermococcales , one of the largest determinants of metabolism and gene expression profiles is the availability of different terminal electron acceptors ( Jäger et al, 2014 ; Mattiroli et al, 2017 ).…”

“…The importance of AHCPs in modulating gene expression suggests unique archaeal gene regulation strategies that take advantage of mechanisms to retain or abolish extended archaeal histone-based chromatin structures ( Sanders et al, 2019b ; Stevens et al, 2020 ; Bowerman et al, 2021 ). To evaluate the normal contribution of AHCPs to gene regulation, we generated strains of the model archaeon Thermococcus kodakarensis ( Farkas et al, 2013 ; Gehring et al, 2017 ; Atomi and Reeve, 2019 ) wherein genomically encoded histone variants impacted global genomic architecture and quantified the gene expression changes resultant from modified AHCP architectures. T. kodakarensis normally encodes two closely related histone isoforms, termed Histone A (HTkA) and Histone B (HTkB), but strains encoding only a single histone variant are viable ( Čuboňová et al, 2012 ; Mattiroli et al, 2017 ; Sanders et al, 2019b ).…”

Thermococcus camini sp. nov., a hyperthermophilic and piezophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Atlantic Ridge

“…Thanks to the different genetic tools available to work on models of Thermococcus species, such as Thermococcus kodakarensis or Thermococcus barophilus for example, many functional studies have been carried out and have allowed significant advances in our knowledge of their metabolism, genomic maintenance mechanisms and biological adaptations, instrumental in advancing our understanding of the biology of the Thermococcales and of the Archaea in general ( e.g . [5, 6]. In addition to being important and ubiquitous players in the hot areas of the hydrothermal ecosystems, Thermococcus species are also of particular interest for learning more about the cellular processes at the limits of life, as this genus contains extremophilic and polyextremophilic organisms, adapted to one or more extreme physical or chemical conditions of their natural habitat.…”

Recent advances in understanding extremophiles

“…Fortunately, there are now model organisms for all extremophile groups mentioned in this review; they include Leptospirillum ferriphilum (acidophile) 54, 55 , Sulfolobus solfataricus (acidophile and thermophile) 56, 57 , Natronomonas pharaonis (alkaliphile and halophile) 58, 59 , Bacillus halodurans (halophile) 60, 61 , H. volcanii (halophile) 62, 63 , Halobacterium sp. NRC-1 (halophile and radiophile) 64, 65 , Wallemia ichthyophaga (halophile) 66, 67 , D. radiodurans (radiophile) 68, 69 , Thermococcus barophilus (piezophile) 70, 71 , Halorubrum lacusprofundi (halophile and psychrophile) 72, 73 , Pseudoalteromonas haloplanktis (psychrophile) 74, 75 , Thermococcus kodakarensis (thermophile) 76, 77 , and Thermus thermophilus (thermophile) 78, 79 .…”