Hydrogenobacter thermophilus

Hydrogenobacter thermophilus TK-6 was originally discovered by Toshiyuki Kawasumi at the Department of Agricultural Chemistry, University of Tokyo in 1980.[2] TK-6 was found with four other previously unknown hydrogen oxidizing bacteria.[2] The bacterium was isolated from hot water containing soils samples from mines of the Izu Peninsula, Japan.[2] The colonies were isolated onto a medium made of 1.5% Bacto-Agar and a specific trace element solution consisting of MoO₃, ZnSO₄·H₂O, CuSO₄·5H₂O, H₃BO₃, MnSO₄·H₂O and CoCl₂·H₂O.[4] Prior to the discovery of Hydrogenobacter thermophilus, only one extremely thermophilic, aerobic and hydrogen-oxidizing bacterium had been described (Bacillus schlegelii).[2] In addition, H. thermophilus has both morphological and physiological differences that vary from processes in B. schegelii, suggesting there are multiple means for being viable in different environments.[2] Until the discovery of H. thermophilus, it was thought that no obligate chemolithotrophic hydrogen oxidizing bacteria existed.[2]

16S rRNA gene sequencing places the family of H. thermophilus, Aquificaceae, in close phylogenetic relationship to the family Aquifex based on 88.5% to 88.9% sequence similarity.[3] H. thermophilus’s next immediate branch point is with the species Caldobacterium hydrogenopailum str. z-823 and the previous divergence branches with Hydrogenobacter strains.[3] Genomic studies of the 16S ribosomal RNA gene in H. thermophilus also suggest that they are part of some of the earliest differentiating orders of bacteria termed the Aquificales.[3] As a result of the early branch point in Aquificales’ genetic history, it indicates that the characteristics of the last common ancestor of life were possibly thermophilic and fixed carbon chemoautotrophically; this gives some direction to the evolution of life.[3]

In 2010, the entire genome of Hydrogenobacter thermophilus TK-6 was sequenced by Hiroyuki Arai et al.[5] Sequencing was done via whole genome shotgun approach through the Sanger sequencing method, and assembled via the Paracel Genome Assembler.[5] It was found to consist of 1,743,135 base pairs arranged in a circular chromosome with an estimated 1,864 protein coding genes and 22 pseudogenes.[5] The genome was found to contain one 16S-23S-5S rRNA operon and 44 tRNA coding genes.[5] The GC content of the genome is 44%,[5] which at the time of its discovery was the lowest among any hydrogen oxidizing bacteria.[2] H. thermophilus contains four gene clusters for membrane-bound hydrogenases.[5] It should also be noted that H. thermophilus lacks the typical PSP (phosphoserine phosphatase) genes involved in amino acid metabolism.[5] In addition, it is an obligate chemolithoautotroph, and so genes commonly used in carbon fixation were present.[5] Genes that encode proteins involved in the RTCA (reductive tricyclic acid cycle) and gluconeogenesis were observed.[5] The sox gene cluster, sqr gene and sorAB genes were also noted, and are involved in the sulfur oxidation protein complex, sulfide:quinone oxidoreductase and sulfite:cytochrome c oxidoreductase respectively.[2] H. thermophilus also contains the necessary genes for nitrate reduction and assimilation.[5]

Hydrogenobacter thermophilus has several unique proteins that allow it to be viable in its environment. Cytochrome b and cytochrome c are present in all strains.[2] H. thermophilus strains also possess a very distinctive sulfur containing quinone, 2-Methylthio-1,4-naphthoquinone.[2] This is the first case of non-Calvin-type pathway that is utilized to convert carbon dioxide into cellular components.[6] In addition to the unique quinone, novel types of phosphoserine phosphatase (PSPs) were discovered and have been analyzed by preliminary crystallization and X-ray diffraction.[7] Both iPSP1 and iPSP2 proteins found in H. thermophilus employ metal-ion-independent pathways while typical PSPs need Mg2+ for activity and are considered to be part of the haloacid dehalogenase-like hydrolase superfamily.[7] iPSP1 is composed of two PspA subunits, while iPSP2 is a heterodimer and has both PspA and PspB subunits.[7] iPSP1 and iPSP2 were observed to share a strong binding affinity towards L-phosphoserine, which supports its activity as a PSP.[7] Novel proteins such as citryl-CoA synthetase (CCS) and ciitryl-CoA (CLL)are utilized within the reductive TCA cycle (Reverse Krebs cycle).[8] These proteins were discovered and characterized through activity purification, SDS-PAGE analysis, and gel filtration chromatography.[8] Additionally, oligionucleotide probes were employed in order to sequence and clone the related genes.[8] The cleavage of citryl-CoA to acetyl-CoA and oxaloacetate occurs in a two step process.[8] First, citryl-coA synthetase catalyzes the formation of citryl-CoA, which is immediately cleaved by citryl-CoA lyase.[8] It was also observed that there is significant level of protein sequence homology between the CCL protein and the C-terminal region of ATP citrate lyase (ACL), an enzyme commonly employed by the reductive TCA cycle.[8]

• Ishii, Masaharu (August 2012). "Crystallization and preliminary X-ray diffraction analysis of a novel type of phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6". Acta Crystallographica Section F. 68 (Part 8): 911–913. doi:10.1107/S1744309112025213. PMC 3412771. PMID 22869120.

• Type strain of Hydrogenobacter thermophilus at BacDive - the Bacterial Diversity Metadatabase