Hydrogenobacter thermophilus
| Hydrogenobacter thermophilus | |
|---|---|
Scientific classification 
| |
| Domain: | Bacteria |
| Phylum: | Aquificota |
| Order: | Aquificales |
| Family: | Aquificaceae |
| Genus: | Hydrogenobacter |
| Species: | H. thermophilus
|
| Binomial name | |
| Hydrogenobacter thermophilus Kawasumi et al. 1984[1]
| |
Hydrogenobacter thermophilus is an extremely thermophilic, straight rod (bacillus) bacterium.[2] TK-6 is the type strain for this species.[2] It is a Gram negative, non-motile, obligate chemolithoautotroph.[2] It belongs to one of the earliest branching order of Bacteria.[3] H. thermophilus TK-6 lives in soil that contains hot water.[2] It was one of the first hydrogen oxidizing bacteria described leading to the discovery, and subsequent examination of many unique proteins involved in its metabolism.[2] Its discovery contradicted the idea that no obligate hydrogen oxidizing bacteria existed, leading to a new understanding of this physiological group.[2] Additionally, H. thermophilus contains a fatty acid composition that had not been observed before.[2]
History
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]
Characterization
Biology
Hydrogenobacter thermophilus is a straight rod (bacillus) bacterium and an extreme thermophile.[2] The size is about .3-.5 microns in width and 2-3 microns in length.[2] Gram staining was done using a Hucker Modification and the reaction was found to be Gram negative.[2] Motility and sporulation were tested using hanging cell method and Dorner method, respectively, and both were found to be negative.[2] The novel fatty acid composition was freed though a nicotinamide adenine dinucleotide phosphate containing solution.[2] The composition was found to be C18:0, C 20:1, 2 carbons longer than any composition seen before.[2] The optimum growth conditions are: temperature between 70 and 75 °C, freshwater, pH around 7.2.[2] The habitat is soil that contains hot, fresh water (70-75 °C) from springs of the Izu Peninsula, Japan.[2]
Metabolism
Hydrogenobacter thermophilus is an obligate chemolithoautotroph.[2] H. thermophilus undergoes aerobic respiration or anaerobic respiration via denitrification.[5] The electron donor is the molecular form of hydrogen, thiosulfate, or elemental sulfur.[5] Nitrogen sources are Ammonium and Nitrate salts.[2] This bacterium utilizes a special form of the reductive tricyclic acid cycle (Reverse Krebs cycle) to fix CO2.[5] Various metabolic processes were examined on a 1.5% Bacto-Agar with various organic compounds, incubated at 50-70 degrees C.[2]
Phylogeny
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]
Genomics
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]
Proteomics
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]
References
- ^ Parte, A.C. "Hydrogenobacter". LPSN.
- ^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa ab Kawasumi, Toshiyuki (1984). "Hydrogenobacter thermophilus gen. nov., sp. nov., an extremely thermophilic, aerobic, hydrogen-oxidizing bacterium". International Journal of Systematic and Evolutionary Microbiology. 34: 5–10. doi:10.1099/00207713-34-1-5.
- ^ a b c d e Pitulle, C; et al. (1994). "Phylogenetic position of Hydrogenobacter". International Journal of Systematic and Evolutionary Microbiology. 44 (4): 620–626. doi:10.1099/00207713-44-4-620. PMID 7981093.
- ^ Kawasumi, Toshiyuki (May 14, 1980). "Isolation of Strictly Thermophilic and Obligately Autotrophic Hydrogen Bacteria". Agricultural and Biological Chemistry. 44 (8): 1985–1986. doi:10.1271/bbb1961.44.1985.
- ^ a b c d e f g h i j k l m Arai, H; et al. (Mar 26, 2010). "Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6". Journal of Bacteriology. 192 (101): 2651–2. doi:10.1128/JB.00158-10. PMC 2863560. PMID 20348262.
- ^ Ishii, M; et al. (1987). "2-Methylthio-1,4-naphthoquinone, a unique sulfur-containing quinone from a thernophilic hydrogen-oxidizing bacterium, Hydrogenobacter therophilus". Journal of Bacteriology. 169 (6): 2380–2384. doi:10.1128/jb.169.6.2380-2384.1987. PMC 212068. PMID 3584059.
- ^ a b c d Chiba, Y; et al. (2012). "Crystallization and preliminary X-ray diffraction analysis of a novel type of phosphoserine phosphatase from Hydrogenbacter thermophilus TK-6". Acta Crystallographica Section F. 68 (Pt 8): 911–913. doi:10.1107/s1744309112025213. PMC 3412771. PMID 22869120.
- ^ a b c d e f Aoshima, M; et al. (2004). "A novel enzyme, citryl-CoA lyase, catalyzing the second step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6". Molecular Microbiology. 52 (3): 763–770. doi:10.1111/j.1365-2958.2004.04010.x. PMID 15101982. S2CID 32105039.
Further reading
- 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.