Pyrobaculum islandicum

A Microbial Biorealm page on the genus Pyrobaculum islandicum

Classification

Higher order taxa

Domain: Archaea

Phylum: Crenarchaeota

Class: Thermoprotei

Order: Thermoproteales

Family: Thermoproteaceae

Genus: Pyrobaculum

Species

NCBI: Taxonomy

Pyrobaculum islandicum

Description and significance

thumb| Pyrobaculum islandicum (DSM 4184) is a rod-shaped hyperthermophilic neutrophilic archaebacteria which was first obtained from boiling sulfataric and geothermal waters in Iceland. The latin root of the name "Pyrobaculum" literally means "firestick", where the syllable "pyro" serves to denote the organism's ability to grow at temperatures above 100°C. The species name "islandicum" denotes Icelandic in relevance to its origin of isolation. [1]

Appearance:

Pyrobaculum islandicum are a gram-negative rod-shaped organism with almost rectangular ends. Cells are usually about 2.5 μm long and exhibit bipolar polytrichous flagellation, each flagellum up to 15 μm long and about 13 nm in width. They occur singly and in V-, X-, and raft-shaped aggregates. They can sometimes be seen with terminal spheres (commonly referred to as "golf-club" structures), which appear during its exponential growth phase. No septa formation has yet been observed during cell division. Pb. islandicum colonies are grey or greenish-black in color. [1]

Habitat/Biotope:

Pyrobaculum islandicum belongs to a family of hyperthermophilic archaebacteria found in continental solfataric springs. Before their discovery, hyperthermophilic bacteria growing at 100°C and above had been isolated exclusively from submarine hydrothermal systems. The surface layer of the solfataras, typically 30 cm thick, is usually rich in sulfate and is relatively acidic (pH 0.5-6). Ferric ion compounds cause a rusty appearance. As you go deeper, the solfataras are usually less acidic and can even be neutral (pH 5-7). Depending on the altitude above sea level, the temperatures can be as high as 100°C. Man-made hot environments can also sometimes serve as suitable environments for hyperthermophiles, such as the boiling outflows of geothermal power plants. Due to the low solubility of oxygen at high temperatures and the presence of reducing gases, most biotopes of hyperthermophiles are anaerobic. [1][3][4]

When the new genus "Pyrobaculum" was first isolated, samples were obtained from an outflow of superheated water of an overpressure valve at the Kafla geothermal power plant and from the Hveragerthi solfatara field (both of which are in Iceland), from the Ribeira Quente solfataras in Azores, and Pisciarelli Solfatara in Italy. The superheated or almost boiling anaerobic solfataric waters from which the organisms were isolated were neutral to slightly alkaline (pH 5-7). Pb. islandicum's low salt tolerance makes them well adapted to the low salt content of the solfataric springs (0-0.5% NaCl), and appears to explain why they are unable to grow within the salty ocean waters of submarine hydrothermal systems. [1]

Significance

Pyrobaculum islandicum is a hyperthermophile that belongs to the third domain of life Archaea, which, from an evolutionary standpoint, may be the most slowly evolving or primitive groups of microorganisms yet discovered. Hyperthermophiles may provide significant insights into the physiological properties of the earliest microorganisms because hyperthermophiles are the only living organisms so closely related to the last common ancestors of modern life. Pyrobactum islandicum's ability to reduce Fe(III) has already led to the suggestion that early microorganisms had the capacity for Fe(III) reduction as well, which coincides with geochemical evidence that pre-biotic Earth was conducive for Fe(III) reduction as one of the earliest means of microbial respiration. [5]

Genome structure

Pyrobaculum islandicum has a circular genome sequence 1.8 Mbp in length and contains 1,978 protein-encoding sequences. The following is a brief description of known sequenced genes from a closely related species, Pyrobaculum aerophilium, that have significance pertaining to most of the phylum Crenarchae and some of the genus Pyrobaculum:

Replication and Repair

The two major mechanisms for avoiding mutations during DNA replication are immediate editing of the growing strand by the DNA polymerase and detection and correction of mismatches soon after replication by the mismatch repair system. High-temperature archaea such as P. aerophilum are an example of organisms that can survive as permanent mutators, which means they are deficient in mismatch repair. This lack of a mismatch repair system is advantageous under certain selective conditions and is a way of generating diversity and responding to ever-changing environments. [6]

DNA Polymerase

Family B polymerases have been found in all archaea. They seem to have multiple family B polymerases that may all play a role at the replication fork. The P. aerophilum genome sequence codes for three family B DNA polymerases, one of each of the B1, B2, and B3 subfamilies. The P. aerophilum B3 DNA polymerase shares 78% amino acid identity to the DNA polymerase of closely related Pyrobaculum islandicum. This enzyme has a 3' to 5' exonuclease activity and, under stable assay conditions for PCR, was shown to amplify DNA fragments of up to 1,500 bp long. Other replication factor homologs detected in the genome were: two copies of the sliding clamp processivity factor, one large subunit, and two copies of the small subunit of the clamp loading protein (replication factor C), DNA ligase, minichromosome maintenance protein, and a possible origin recognition protein (orc/cdc6). [6]

Cell Division

No homologs of FtsZ have been found within the crenarchaea. A type of "snapping division" may be an example of a crenarchaeal FtsZ independent mechanism. [6]

Cell structure and metabolism

Cell Structure

Pyrobaculum islandicum, as stated previously, are rod-shaped with polytrichous flagellation located on each pole of the organism. The cells are usually 2.5 μm long, while each flagellum are up to 15 μm long and about 13 nm in width. As with most archaebacteria, they lack a murein cell wall and instead have a protein cell envelope. In addition, they have isopranyl ether lipids, and the existence of an ADP-ribosylable elongation factor G. [1]

Pyrobaculum islandicum also has the enzyme glutamate dehydrogenase (GluDH), which is a hyperthermostable NAD-dependent GluDH. This enzyme plays a major function as an adaptive mechanism that allows the organim's metabolism to function and the biomolecules, such as proteins, enzymes, and DNA to remain intact even at extremely high temperatures. GluDH is not inactivated by incubation at 100°C, and is highly resistant to denaturants, organic solvents, and detergents, such as guanidine, hydrochloride, urea, ethanol, methanol, DMF, and DOC, at 50°C. [2]

Metabolism

Pyrobaculum islandicum is a strict anaerobe, that grows optimally at 100°C, at which its population will double every 280 minutes (in closed culture vessels). Within its superheated biotope, it may act as a primary producer of organic matter during chemolithoautotrophic growth on S⁰, CO₂ , and H₂. It is also facultatively organotrophic. In the presence of organic material, it is able to also use other S-compounds like thiosulfate and sulfate present in geothermal waters. During organotrophic growth, S⁰, thiosulfate, sulfite, L(-)-cystine and oxidized glutathione serve as electron acceptors. [1]

All hyperthermophiles that have been studied have a constitutive ability to reduce Fe(III). Pyrobaculum islandicum can reduce Fe(III) oxide to Fe(II), as well as reduce a variety of other metals. P. islandicum and P. aerophilum are the only Archaea that have been shown to conserve energy to support growth from dissimilatory Fe(III) reduction. With hydrogen as the electron donor and Fe(III) citrate as the electron acceptor, an increase in cell numbers was reported 10-fold higher. In contrast with P. islandicum's ability to grow autotrophically with hydrogen and S⁰ as the electron acceptor, it has not been found to be capable of autotrophic growth with hydrogen and Fe(III) - small amounts of yeast extract are still required for growth during laboratory studies. [5]

Pyrobaculum islandicum cannot utilize sugars as electron donors. During organotrophic growth, thiosulfate or elemental sulfur can serve as a terminal electron acceptor. The only fermentation products detected during organotrophic growth are CO₂ and H₂S rather than organic acids. In cell extracts of P. islandicum, all enzymes of the citric acid cycle (other than monoxide dehydrogenase) were detected, which indicates that oxidation of acetyl-CoA to CO₂ proceeds via the citric acid cycle rather than by the acetyl-CoA/carbon monoxide dehydrogenase pathway. [7]

Ecology

Pyrobaculum islandicum acts as a primary producer by growing chemolithoautotrophically on inorganic energy sources and CO₂ as a sole carbon source. It acts as a consumer as well by growing faculatively hetertrophically by using a variety of electron donors and acceptors, thus making it more metabolically versatile. This property is important for efficient competition within its ecosystem. [4]

Many of the metals and metalloids that P. islandicum reduces to less-soluble forms are considered environmental contaminants. By converting them to less soluble forms, these contaminat metals are less mobile in groundwater and can be precipitated from waste streams or soil washings. The reduction of these contaminant metals by Fe(III)-reducing microorgansims, such as P. islandicum, has been shown to have potential for the removal of these contaminant metals from waters and waste streams and to immobilize metals in subsurface environments. [5]

Pathology

Pyrobaculum islandicum does not have any known pathogenic effects and thus does not cause any known disease among humans. It has been discovered, however, that it is resistant to the antibiotics penicillin, streptomycin, phosphomycin, vancomycin, and chloramphenicol. The cells are also sensitive to rifampicin. This sensitivity is unusual for archaebacteria and may be possibly explained by a target different from the RNA polymerase similar to Halobacterium halobium. [1]

Application to Biotechnology

GluDH

The NAD-dependent GluDH produced by Pb. islandicum may be expected to be more preferable for application than the NADP-dependent enzyme, because NAD and NADH are much cheaper than NADP and NADPH, respectively. Also, the enzyme's hyperthermostability and resistance to denaturants suggests that it may be preferred in applications as a reagent for biosensor and bioreactor processes under some special conditions. [2]

Current Research

Characterization of malate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum. [May 9, 2007]

Yennaco LJ, et.al. attempt to study the effects of native and recombinant malate dehydrogenase (MDH) obtained from Pyrobaculum islandicum. They try to test the catalytic efficiency of oxaloacetate reduction by P. islandicum MDH.

Citric acid cycle in the hyperthermophilic archaeon Pyrobaculum islandicum grown autotrophically, heterotrophically, and mixotrophically with acetate. [June 2006]

Hu Y, et.al. try to gain a better understanding of the control of carbon flow during P. islandicum's uses of the citric acid cycle in the oxidative and reductive directions for heterotrophic and autotrophic growth, respectively.

Intersubunit interaction induced by subunit rearrangement is essential for the catalytic activity of the hyperthermophilic glutamate dehydrogenase from Pyrobaculum islandicum. [November 2005]

Goda S, et.al. suggest that activation of the Pyrobaculum islandicum glutamate dehydrogenase (pis-GDH) cannot occur unless there is a subunit rearrangement, such as to a quaternary structure of the hexameric recombinant pis-GDH.

References

[1] Huber, R., Kristjansson, J.K., and Stetter, K.O. "Pyrobaculum gen. nov., a new genus of neutrophilic, rod-shaped archaebacteria from continental solfataras growing optimally at 100°C". Archives of Microbiology. December 1987. Volume 149. p. 95-101. http://www.springerlink.com/content/j7016363n25h5221/fulltext.pdf

[2] Kujo, C., and Ohshima, T. "Enzymological Characteristics of the Hyperthermostable NAD-Dependent Glutamate Dehydrogenase from the Archaeon Pyrobaculum islandicum and Effects of Denaturants and Organic Solvents". Applied and Environmental Microbiology. June 1998. Volume 64. p. 2152-2157. http://aem.asm.org/cgi/reprint/64/6/2152

[3] Stetter, K.O., Fiala, G., Huber, Huber, R., and Segerer, A. "Hyperthermophilic microorganisms". FEMS Microbiology Letters. June 1990. Volume 75. p. 117-124. http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1574-6968.1990.tb04089.x

[4] Segerer, A., Burggraf, S., Fiala, G., Huber, H., Huber, R., Pley, U., and Stetter, K. "Life in Hot Springs and Hydrothermal Vents". Origins of Life and Evolution of Biospheres. February 1993. Volume 23. p. 77-90. http://www.springerlink.com/content/x5x48t32qt6g7q67/fulltext.pdf

[5] Kashefi, K., and Lovley, D.R. "Reduction of Fe(III), Mn(IV), and Toxic Metals at 100°C by Pyrobaculum islandicum". Applied and Environmental Microbiology. March 2000. Volume 66. p. 1050-1056. http://aem.asm.org/cgi/reprint/66/3/1050

[6] Sorel T. Fitz-Gibbon, Heidi Ladner, Ung-Jin Kim, Karl O. Stetter, Melvin I. Simon, and Jeffrey H. Miller. "Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum". PNAS. January 22, 2002. Volume 99. p. 984-989. http://www.pnas.org/cgi/reprint/99/2/984

[7] Selig, M., and Schonheit, P. "Oxidation of organic compounds to CO₂ with sulfur or thiosulfate as electron acceptor in the anaerobic hyperthermophilic archaea Thermoproteus tenax and Pyrobaculum islandicum proceeds via the citric acid cycle". Archives of Microbiology. October 1994. Volume 162. p. 286-294. http://www.springerlink.com/content/jx83535710hjj831/fulltext.pdf

Edited by Joseph Yang, student of Professor Rachel Larsen, UCSD [1]