Hydrogenobacter thermophilus

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Hydrogenobacter thermophilus
Scientific classification OOjs UI icon edit-ltr.svg
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]

Contents

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]

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References

  1. ↑ Parte, A.C. "Hydrogenobacter". LPSN .
  2. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 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 .
  3. 1 2 3 4 5 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.
  4. ↑ 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 .
  5. 1 2 3 4 5 6 7 8 9 10 11 12 13 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.
  6. ↑ Ishii, M; et al. (1987). "2-Methylthio-1,4-napthoquinone, 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.
  7. 1 2 3 4 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.
  8. 1 2 3 4 5 6 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.

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