Pyrobaculum islandicum: Difference between revisions
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==Genome structure== | ==Genome structure== | ||
Only the genome of one closely related species to ''Pyrobaculum islandicum'', ''Pyrobaculum aerophiluim'', has been sequenced thus far. It has a circular genome sequence 2,222,430 base pairs in length and contains 2605 protein-encoding sequences. The following is a brief description of sequenced genes from this species that have significance pertaining to most of the | Only the genome of one closely related species to ''Pyrobaculum islandicum'', ''Pyrobaculum aerophiluim'', has been sequenced thus far. It has a circular genome sequence 2,222,430 base pairs in length and contains 2605 protein-encoding sequences. The following is a brief description of known sequenced genes from this species that have significance pertaining to most of the phylum ''Crenarchae'' and some of the genus ''Pyrobaculum'': | ||
'''Replication and Repair''' | '''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 and metabolism== | ||
Revision as of 08:17, 29 August 2007
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
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NCBI: Taxonomy |
Pyrobaculum islandicum
Description and significance
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
Only the genome of one closely related species to Pyrobaculum islandicum, Pyrobaculum aerophiluim, has been sequenced thus far. It has a circular genome sequence 2,222,430 base pairs in length and contains 2605 protein-encoding sequences. The following is a brief description of known sequenced genes from this species 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
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.
Ecology
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.
Pathology
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.
Application to Biotechnology
Does this organism produce any useful compounds or enzymes? What are they and how are they used?
Current Research
Enter summaries of the most recent research here--at least three required
References
Edited by student of Rachel Larsen
