Hydrogenobacter thermophilus

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Hydrogenobacter thermophilus
Scientific classification
Kingdom: Bacteria
Division: Aquificae
Class: Aquificales
Order: Aquificales
Family: Aquificaceae
Genus: Hydrogenobacter
Species: H. thermophilus
Binomial name
Hydrogenobacter thermophilus

Hydrogenobacter thermophilus is an extremely thermophilic, straight rod (bacillus) bacterium.[1] TK-6 is the type strain for this species.[1] It is a Gram negative, non-motile, obligate chemolithoautotroph.[1] It belongs to one of the earliest branching order of Bacteria.[2] H. thermophilus TK-6 lives in soil that contains hot water.[1] 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.[1] Its discovery contradicted the idea that no obligate hydrogen oxidizing bacteria existed, leading to a new understanding of this physiological group.[1] Additionally, H. thermophilus contains a fatty acid composition that had not be observed before.[1]

History[edit]

Hydrogenobacter thermophilus TK-6 was originally discovered by Toshiyuki Kawasumi at the Department of Agricultural Chemistry, University of Tokyo in 1980.[1] TK-6 was found with four other previously unknown hydrogen oxidizing bacteria.[1] The bacterium was isolated from hot water containing soils samples from mines of the Izu Peninsula, Japan.[1] The colonies were isolated onto a medium made of 1.5% Bacto-Agar and a specific trace element solution consisting of MoO3, ZnSO,H20, CuSO4-E5H2O, H3B03,MnSO4-5H20 and CoC12-E6H20.[3] Prior to the discovery of Hydrogenobacter thermophilus, only one extremely thermophilic, aerobic and hydrogen-oxidizing bacterium had been described (Bacillus schegelii).[1] 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.[1] Until the discovery of H. thermophilus, it was thought that no obligate chemolithotrophic hydrogen oxidizing bacteria existed.[1]

Characterization[edit]

Biology[edit]

Hydrogenobacter thermophilus is a straight rod (bacillus) bacterium and an extreme thermophile.[1] The size is about .3-.5 microns in width and 2-3 microns in length.[1] Gram staining was done using a Hucker Modification and the reaction was found to be Gram negative.[1] Motility and sporulation were tested using hanging cell method and Dorner method, respectively, and both were found to be negative.[1] The novel fatty acid composition was freed though a nicotinamide adenine dinucleotide phosphate containing solution.[1] The composition was found to be C18:0, C 20:1, 2 carbons longer than any composition seen before.[1] The optimum growth conditions are: temperature between 70 and 75 °C, freshwater, pH around 7.2.[1] The habitat is soil that contains hot, fresh water (70-75 °C) from springs of the Izu Peninsula, Japan.[1]

Metabolism[edit]

Hydrogenobacter thermophilus is an obligate chemolithoautotroph.[1] H. thermophilus undergoes aerobic respiration or anaerobic respiration via denitrification.[4] The electron donor is the molecular form of hydrogen, thiosulfate, or elemental sulfur.[4] Nitrogen sources are Ammonium and Nitrate salts.[1] This bacterium utilizes a special form of the reductive tricyclic acid cycle (Reverse Krebs cycle) to fix CO2.[4] Various metabolic processes were examined on a 1.5% Bacto-Agar with various organic compounds, incubated at 50-70 degrees C.[1]

Phylogeny[edit]

16S rRNA gene sequencing places the family of H. thermolphilus, Aquificaceae, in close phylogenetic relationship to the family Aquifex based on 88.5% to 88.9% sequence similarity.[2] H. thermophilus’s next immediate branch point is with the species Caldobacterium hydrogenopailum str. z-823 and the previous divergence branches with Hydrogenobacter strains.[2] 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.[2] 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.[2]

Genomics[edit]

In 2010, the entire genome of Hydrogenobacter thermophilus TK-6 was sequenced by Hiroyuki Arai et al.[4] Sequencing was done via whole genome shotgun approach through the Sanger sequencing method, and assembled via the Paracel Genome Assembler.[4] 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.[4] The genome was found to contain one 16S-23S-5S rRNA operon and 44 tRNA coding genes.[4] The GC content of the genome is 44%,[4] which at the time of its discovery was the lowest among any hydrogen oxidizing bacteria.[1] H. thermophilus contains four gene clusters for membrane-bound hydrogenases.[4] It should also be noted that H. thermophilus lacks the typical PSP (phosphoserine phosphatase) genes involved in amino acid metabolism.[4] In addition, it is an obligate chemolithoautotroph, and so genes commonly used in carbon fixation were present.[4] Genes that encode proteins involved in the RTCA (reductive tricyclic acid cycle) and gluconeogenesis were observed.[4] 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.[1] H. thermophilus also contains the necessary genes for nitrate reduction and assimilation.[4]

Proteomics[edit]

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.[1] H. thermophilus strains also possess a very distinctive sulfur containing quinone, 2-Methylthio-1,4-naphthoquinone.[1] This is the first case of non-Calvin-type pathway that is utilized to convert carbon dioxide into cellular components.[5] 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.[6] 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.[6] iPSP1 is composed of two PspA subunits, while iPSP2 is a heterodimer and has both PspA and PspB subunits.[6] iPSP1 and iPSP2 were observed to share a strong binding affinity towards L-phosphoserine, which supports its activity as a PSP.[6] Novel proteins such as citryl-CoA synthetase (CCS) and ciitryl-CoA (CLL)are utilized within the reductive TCA cycle (Reverse Krebs cycle).[7] These proteins were discovered and characterized through activity purification, SDS-PAGE analysis, and gel filtration chromatography.[7] Additionally, oligionucleotide probes were employed in order to sequence and clone the related genes.[7] The cleavage of citryl-CoA to acetyl-CoA and oxaloacetate occurs in a two step process.[7] First, citryl-coA synthetase catalyzes the formation of citryl-CoA, which is immediately cleaved by citryl-CoA lyase.[7] 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.[7]

References[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ Kawasumi, Toshiyuki (May 14, 1980). "Isolation of Strictly Thermophilic and Obligately Autotrophic Hydrogen Bacteria". Agricultural Biology, Chemistry 44: 1985–1986. 
  4. ^ 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. 
  5. ^ 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. 
  6. ^ 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 theromphilus TK-6". Structural Biology and Crystallization Communications 68: 911–913. 
  7. ^ 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. 

Further reading[edit]