Pyrococcus horikoshii: Difference between revisions
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Higher Order Taxa | |||
'''Classification:''' | |||
'''Higher Order Taxa''' | |||
Domain: Archaea; Phylum: Euryarchaeota; Class: Thermococci ; Order: Thermococcales ; Family: Thermococcaceae ; Genus: Pyrococcus (3). | Domain: Archaea; Phylum: Euryarchaeota; Class: Thermococci ; Order: Thermococcales ; Family: Thermococcaceae ; Genus: Pyrococcus (3). | ||
Species | Species | ||
Pyrococcus horikoshii | ''Pyrococcus horikoshii'' | ||
'''Description and Significance ''' | |||
''Pyrococcus horikoshii'' thrives at an optimal temperature of 98 °C and dwells at a depth of 1395m, categorizing it has a hyperthermophilic extermophiles, one of four species with the same characteristics from the ''Pyrococcous'' genus. (4) In the ''Pyrcoccous'' genus, species all dwell at an optimal growth temperature of nearly 100 °C, greater than others from the Archaea genera, as well as dwell at a great sea depth than the other arcahaeons (7). ''Pyrococcus horikoshii'' is also obligately heterotrophic, as well as an obligate anaerobe (6). | |||
''Pyrococcus horikoshii'' OT3 was first isolated from a hydrothermal fluid sample obtained from the Okinawa Trough vents in the Pacific Ocean (4). The sample strain was then analyze and sequenced by assembling the sequence of the physical map-based contigs of fosmid clones, and then gap-filled was preformed with long polymeraze chain reaction (PCR) products. Of the 2061 total open reading frames (ORFs) assigned, 1202 ORFs (58.3%) did not show any significant similarities to any sequences from the databases (6). | |||
The proteins and enzymes produced by ''Pyrococcus horikoshii'' exhibit great heat resistant qualities, and are being utilized for these qualities in the different industrial fields of chemistry, food, and medical supplies (2). | |||
'''Genomic Structure''' | |||
The entire genome of ''Pyrococcus horikoshii'' was 1,738,505 bp in length, which is the smallest of the 3 already sequenced ''Pyrococcus'' species, ''P. furiosus'' and ''P. abyssi''. The G-C (guanine-cytosine) content is 41.9%. A total of 2061 ORFs (open reading frames) were assigned as protein-coding regions, 406 (19.7%) of which showed similarity to searches against databases, 453 (22.0%) sequenced without known functions, and 1202 (58.3%) with no significant similarity to any sequences from databases. Only 3% of the sequenced ORF assigned were organism specific, most of which were conserved in ''P. abyssi, P. furiosus, and Thermococcus kodakaraensis''. Of the RNA genes identified one was 16S-23S rRNA operon, two were 5S rRNA genes and 46 were tRNA genes (6). Phylogenetic analysis of the 16S rRNA encoding sequences classified the isolate sample into the genus ''Pyrococcus'' (5). Genes from ''Pyrococcus horikoshii'' were also found to be homologous to the mammalian gene for an acylamino acid-releasing enzyme, in which provide evidence that mechanisms of protein degradation and/or initiation of protein synthesis in archaea may be similar to those in eukaryotes (8). | |||
'''Cell Structure and Metabolism''' | |||
Pyrococcus horikoshii | ''Pyrococcus horikoshii'' are irregularly shaped cocci, containing a tuft of flagella. In transmission electron microscopy of the cell wall, ''Pyrococcus horikoshii'' was shown to have a periplasmic space, similar to the envelope of the ''P. furiosus''. The main cell membrane component is tetraether lipid, with small amounts of diether lipids (4). | ||
Pyrococcus | Peptide fermentation is the principle metabolic pathway for the ''Pyrococcus'' genus. In culture ''Pyrococcus horikoshi'' utilizes a complex media of proteins, consisting of peptone, tryptone, yeast extract, or a 21-amino-acid mixture supplemented with vitamins (4). The genus is also an obligate anaerobe and obligately heterotrophic (9). For optimal growth and metabolism, the ''Pyrococcus' genus utilizes sulfur; however sulfur is not necessary for growth (4). ''Pyrococcus horikoshii'' is auxotrophic for tryptophan and histidine (10), in contrast to ''P. furiosus'' and ''P. abyssi'', in which tryptophan is not required (4). Mechanisms for protein degradation and initiation of protein synthesis utilize acylamino acid-releasing enzyme, in which was found to be homologous to those found in eukaryotes (8). Being obligate anaerobic, ''Pyrococcus horikoshii'' is trigger to go into peroxide detoxification during exposure to oxygen. Oxygen sensitivity causes proteins to form thioredoxin-dependent system to eliminate reactive oxygen species in ''P. horikoshii'' (9). | ||
'''Ecology''' | |||
Pyrococcus horikoshii | ''Pyrococcus horikoshii'' was first isolated from Okinawa Trough vents in the Pacific Ocean, at depths of 1395m (4). Being considered a hyperthermophilic extremophile, ''Pyrococcus horikoshii'' survives at temperatures between 88°C and 104°C with the optimal temperature of 98°C and dwells at pressures of nearly 200 atm (6). , Due to such high boiling point temperatures being able to not harbor any usable oxygen, ''Pyrococcus horikoshii'' is an obligate anaerobe, and is unable to grow with the presence of oxygen. Optimal growth was shown to be at pH 7, with a range of pH 5-8, and a NaCl concentration 2.4% , range 1%-5% (4). Sulfur also enhances growth (6). | ||
'''Pathology''' | |||
Pyrococcus horikoshii | There are no known diseases that are caused by this organism. The surviving temperature for ''Pyrococcus horikoshii'', 98°C, is well over the surviving temperature for mammals and has not been found to be pathogenic. | ||
'''Application to Biotechnology''' | |||
''Pyrococcus horikoshii'' exhibits hyperthermophilic characteristics, in which have been utilized in various industrial fields, including chemisstry, food, and medical supplies. The hyperthermophilic survival capacity allows the Pyrococcus horikoshii to produce enzymes and proteins in which have great heat resistance, and therefore have great stability at high temperatures (6). | |||
Pyrococcus horikoshii | ''Pyrococcus horikoshii'' has been utilized for its hyperthermostable qualities to create high thermostable gene products (6), extreme temperature adaptable PPases for biotechnology applications (11), as well for hyperthermostable endoglucanase, which hydrolyzes celluloses for biopolishing of cotton products, an essential step in removing fuzz from fabrics, in order to give a soft and clean appearance (7). ''Pyrococcus horikoshii'' is also being utilized for its gene homology to a gene for AARE from pig liver (8). | ||
Current Research | '''Current Research''' | ||
[1] In an attempt to elucidate the mechanism for the enzymatic reaction of putative UDP-N-acetyl-d-mannosamine dehydrogenase (UDPManNAcDH), an essential enzyme for polysaccharide biosynthesis, UDPManNAcDH was taken from Pyrococcus horikoshii OT3, and was expressed in Escherichia coli and purified. Through the process of purification, crystallization, and crystallographic analysis of putative UDPManNAcDH from Pyrococcus horikoshii OT3, and deeper understanding of the chemical principles of the biosynthesis of UDPManNAcDH was done, in order to analyze its function in the catalyzation of NAD+- (12). | '''[1]''' In an attempt to elucidate the mechanism for the enzymatic reaction of putative UDP-N-acetyl-d-mannosamine dehydrogenase (UDPManNAcDH), an essential enzyme for polysaccharide biosynthesis, UDPManNAcDH was taken from ''Pyrococcus horikoshii OT3'', and was expressed in Escherichia coli and purified. Through the process of purification, crystallization, and crystallographic analysis of putative UDPManNAcDH from ''Pyrococcus horikoshii OT3'', and deeper understanding of the chemical principles of the biosynthesis of UDPManNAcDH was done, in order to analyze its function in the catalyzation of NAD+- (12). | ||
Using biotin carboxyl carrier protein and biotin protein ligase complexes from Pyrococcus horikoshii OT3, the details of the protein-protein interactions were examined in the biotinylation function of the C-terminal half fragment of BCCP, the R48A mutant of BPL and the R48A K111A double mutant of BPL. This is first done by expressing, purifying and crystallizing the biotin carboxyl carrier protein and biotin protein ligase complexes from Pyrococcus horikoshii OT3 (13). | '''[2]'''Using biotin carboxyl carrier protein and biotin protein ligase complexes from ''Pyrococcus horikoshii OT3'', the details of the protein-protein interactions were examined in the biotinylation function of the C-terminal half fragment of BCCP, the R48A mutant of BPL and the R48A K111A double mutant of BPL. This is first done by expressing, purifying and crystallizing the biotin carboxyl carrier protein and biotin protein ligase complexes from ''Pyrococcus horikoshii OT3'' (13). | ||
[3] In Pyrococcus horikoshii a gene for a putative protein-disulfide oxidoreductase (phdsb) was isolated and characterized. In an attempt to find similarities between DsbA-like proteins of archaea and bacteria, first the genomic structure was analyzed. In Pyrococcus horikoshii the phdsb gene contained open reading frame encoding a protein with an “NH2-terminal extension similar to the bacterial signal peptides.” In examining the conserved sequence motifs in members of the bacterial DsbA family, no connection was found. However, when analyzing recombinant protein structures, the mature form of PhDsb behaved as a activities of in vitro DsbA of Escherichia coli. “Thus, in spite of their low overall sequence similarities, DsbA-like proteins of archaea and bacteria were found to be highly similar in terms of function (14). | '''[3]''' In ''Pyrococcus horikoshii'' a gene for a putative protein-disulfide oxidoreductase (phdsb) was isolated and characterized. In an attempt to find similarities between DsbA-like proteins of archaea and bacteria, first the genomic structure was analyzed. In ''Pyrococcus horikoshii'' the phdsb gene contained open reading frame encoding a protein with an “NH2-terminal extension similar to the bacterial signal peptides.” In examining the conserved sequence motifs in members of the bacterial DsbA family, no connection was found. However, when analyzing recombinant protein structures, the mature form of PhDsb behaved as a activities of in vitro DsbA of Escherichia coli. “Thus, in spite of their low overall sequence similarities, DsbA-like proteins of archaea and bacteria were found to be highly similar in terms of function (14). | ||
'''References''' | |||
1. | 1. http://www.umbi.umd.edu/~comb/facilities/fermentation/Images/ot3.jpeg [permission pending] | ||
2. http://wishart.biology.ualberta.ca/BacMap/cgview_linked_maps/NC_000961/png/1_1.png [permission granted] | 2. http://wishart.biology.ualberta.ca/BacMap/cgview_linked_maps/NC_000961/png/1_1.png [permission granted] | ||
3. NCBI: Taxonomy. <http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=134> | 3. NCBI: Taxonomy. <http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=134> | ||
Latest revision as of 03:31, 20 August 2010
Classification:
Higher Order Taxa Domain: Archaea; Phylum: Euryarchaeota; Class: Thermococci ; Order: Thermococcales ; Family: Thermococcaceae ; Genus: Pyrococcus (3).
Species Pyrococcus horikoshii
Description and Significance
Pyrococcus horikoshii thrives at an optimal temperature of 98 °C and dwells at a depth of 1395m, categorizing it has a hyperthermophilic extermophiles, one of four species with the same characteristics from the Pyrococcous genus. (4) In the Pyrcoccous genus, species all dwell at an optimal growth temperature of nearly 100 °C, greater than others from the Archaea genera, as well as dwell at a great sea depth than the other arcahaeons (7). Pyrococcus horikoshii is also obligately heterotrophic, as well as an obligate anaerobe (6).
Pyrococcus horikoshii OT3 was first isolated from a hydrothermal fluid sample obtained from the Okinawa Trough vents in the Pacific Ocean (4). The sample strain was then analyze and sequenced by assembling the sequence of the physical map-based contigs of fosmid clones, and then gap-filled was preformed with long polymeraze chain reaction (PCR) products. Of the 2061 total open reading frames (ORFs) assigned, 1202 ORFs (58.3%) did not show any significant similarities to any sequences from the databases (6).
The proteins and enzymes produced by Pyrococcus horikoshii exhibit great heat resistant qualities, and are being utilized for these qualities in the different industrial fields of chemistry, food, and medical supplies (2).
Genomic Structure
The entire genome of Pyrococcus horikoshii was 1,738,505 bp in length, which is the smallest of the 3 already sequenced Pyrococcus species, P. furiosus and P. abyssi. The G-C (guanine-cytosine) content is 41.9%. A total of 2061 ORFs (open reading frames) were assigned as protein-coding regions, 406 (19.7%) of which showed similarity to searches against databases, 453 (22.0%) sequenced without known functions, and 1202 (58.3%) with no significant similarity to any sequences from databases. Only 3% of the sequenced ORF assigned were organism specific, most of which were conserved in P. abyssi, P. furiosus, and Thermococcus kodakaraensis. Of the RNA genes identified one was 16S-23S rRNA operon, two were 5S rRNA genes and 46 were tRNA genes (6). Phylogenetic analysis of the 16S rRNA encoding sequences classified the isolate sample into the genus Pyrococcus (5). Genes from Pyrococcus horikoshii were also found to be homologous to the mammalian gene for an acylamino acid-releasing enzyme, in which provide evidence that mechanisms of protein degradation and/or initiation of protein synthesis in archaea may be similar to those in eukaryotes (8).
Cell Structure and Metabolism
Pyrococcus horikoshii are irregularly shaped cocci, containing a tuft of flagella. In transmission electron microscopy of the cell wall, Pyrococcus horikoshii was shown to have a periplasmic space, similar to the envelope of the P. furiosus. The main cell membrane component is tetraether lipid, with small amounts of diether lipids (4).
Peptide fermentation is the principle metabolic pathway for the Pyrococcus genus. In culture Pyrococcus horikoshi utilizes a complex media of proteins, consisting of peptone, tryptone, yeast extract, or a 21-amino-acid mixture supplemented with vitamins (4). The genus is also an obligate anaerobe and obligately heterotrophic (9). For optimal growth and metabolism, the Pyrococcus' genus utilizes sulfur; however sulfur is not necessary for growth (4). Pyrococcus horikoshii is auxotrophic for tryptophan and histidine (10), in contrast to P. furiosus and P. abyssi, in which tryptophan is not required (4). Mechanisms for protein degradation and initiation of protein synthesis utilize acylamino acid-releasing enzyme, in which was found to be homologous to those found in eukaryotes (8). Being obligate anaerobic, Pyrococcus horikoshii is trigger to go into peroxide detoxification during exposure to oxygen. Oxygen sensitivity causes proteins to form thioredoxin-dependent system to eliminate reactive oxygen species in P. horikoshii (9).
Ecology
Pyrococcus horikoshii was first isolated from Okinawa Trough vents in the Pacific Ocean, at depths of 1395m (4). Being considered a hyperthermophilic extremophile, Pyrococcus horikoshii survives at temperatures between 88°C and 104°C with the optimal temperature of 98°C and dwells at pressures of nearly 200 atm (6). , Due to such high boiling point temperatures being able to not harbor any usable oxygen, Pyrococcus horikoshii is an obligate anaerobe, and is unable to grow with the presence of oxygen. Optimal growth was shown to be at pH 7, with a range of pH 5-8, and a NaCl concentration 2.4% , range 1%-5% (4). Sulfur also enhances growth (6).
Pathology
There are no known diseases that are caused by this organism. The surviving temperature for Pyrococcus horikoshii, 98°C, is well over the surviving temperature for mammals and has not been found to be pathogenic.
Application to Biotechnology
Pyrococcus horikoshii exhibits hyperthermophilic characteristics, in which have been utilized in various industrial fields, including chemisstry, food, and medical supplies. The hyperthermophilic survival capacity allows the Pyrococcus horikoshii to produce enzymes and proteins in which have great heat resistance, and therefore have great stability at high temperatures (6).
Pyrococcus horikoshii has been utilized for its hyperthermostable qualities to create high thermostable gene products (6), extreme temperature adaptable PPases for biotechnology applications (11), as well for hyperthermostable endoglucanase, which hydrolyzes celluloses for biopolishing of cotton products, an essential step in removing fuzz from fabrics, in order to give a soft and clean appearance (7). Pyrococcus horikoshii is also being utilized for its gene homology to a gene for AARE from pig liver (8).
Current Research
[1] In an attempt to elucidate the mechanism for the enzymatic reaction of putative UDP-N-acetyl-d-mannosamine dehydrogenase (UDPManNAcDH), an essential enzyme for polysaccharide biosynthesis, UDPManNAcDH was taken from Pyrococcus horikoshii OT3, and was expressed in Escherichia coli and purified. Through the process of purification, crystallization, and crystallographic analysis of putative UDPManNAcDH from Pyrococcus horikoshii OT3, and deeper understanding of the chemical principles of the biosynthesis of UDPManNAcDH was done, in order to analyze its function in the catalyzation of NAD+- (12).
[2]Using biotin carboxyl carrier protein and biotin protein ligase complexes from Pyrococcus horikoshii OT3, the details of the protein-protein interactions were examined in the biotinylation function of the C-terminal half fragment of BCCP, the R48A mutant of BPL and the R48A K111A double mutant of BPL. This is first done by expressing, purifying and crystallizing the biotin carboxyl carrier protein and biotin protein ligase complexes from Pyrococcus horikoshii OT3 (13).
[3] In Pyrococcus horikoshii a gene for a putative protein-disulfide oxidoreductase (phdsb) was isolated and characterized. In an attempt to find similarities between DsbA-like proteins of archaea and bacteria, first the genomic structure was analyzed. In Pyrococcus horikoshii the phdsb gene contained open reading frame encoding a protein with an “NH2-terminal extension similar to the bacterial signal peptides.” In examining the conserved sequence motifs in members of the bacterial DsbA family, no connection was found. However, when analyzing recombinant protein structures, the mature form of PhDsb behaved as a activities of in vitro DsbA of Escherichia coli. “Thus, in spite of their low overall sequence similarities, DsbA-like proteins of archaea and bacteria were found to be highly similar in terms of function (14).
References
1. http://www.umbi.umd.edu/~comb/facilities/fermentation/Images/ot3.jpeg [permission pending] 2. http://wishart.biology.ualberta.ca/BacMap/cgview_linked_maps/NC_000961/png/1_1.png [permission granted] 3. NCBI: Taxonomy. <http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=134> 4. González, J.M., Masuchi, Y., Robb, F.T., Ammerman, J.W., Maeder, D.L., Yanagibayashi, M., Tamaoka, J., and Kato, C. “Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough.” Extremophiles. 1998 May. Volume 2(2). p. 123-30. <http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=9672687&dopt=AbstractPlus> 5. Chinen, A., Uchiyama, I., and Kobayashi, I. “Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction–modification genes with large genome polymorphisms” Gene. 2000 December. Volume 259(1-2). P.109-121. <http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-423RGKS-G&_user=4429&_coverDate=12%2F23%2F2000&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059602&_version=1&_urlVersion=0&_userid=4429&md5=57c4673850046a581c2f060b5ab67e30> 6. Kawarabayasi, Y., Sawada, M., Horikawa, H., Haikawa, Y., Hino, Y., Yamamoto, S., Sekine, M., Baba, S., Kosugi, H., Hosoyama, A., Nagai, Y., Sakai, M., Ogura, K., Otsuka, R., Nakazawa, H., Takamiya, M., Ohfuku, Y., Funahashi, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Aoki, K., Kikuchi, H. “Complete Sequence and Gene Organization of the Genome of a Hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3.” DNA Res. 1998 April. Volume 5(2). p. 55-76. <http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=9679194&dopt=Abstract%20target%3D> 7. Ando, S., Ishida, H., Kosugi, Y. and Ishikawa, K. “Hyperthermostable Endoglucanase from Pyrococcus horikoshii.” Appl Environ Microbiol. 2002 January. Volume 68(1). p 430–433. <http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=126571#r4> 8. Ishikawa, K., Ishida, H., Koyama, Y., Kawarabayasi, Y., Kawahara, J., Matsui, E., and Matsui, I. “Acylamino Acid-releasing Enzyme from the Thermophilic Archaeon Pyrococcus horikoshii.” Biol Chem 1998 July Volume 273(28). p. 17726-17731, 10. http://www.jbc.org/cgi/content/abstract/273/28/17726 9. Kashima, Y., and Ishikawa, K. “Alkyl Hydroperoxide Reductase Dependent on Thioredoxin-Like Protein from Pyrococcus horikoshii” J. Biochem. 2003. Volume 134(1). p. 25-29. < http://jb.oxfordjournals.org/cgi/content/full/134/1/25> 10. Maeder, D., Weiss, R., Dunn, D., Cherry, J., González, J., DiRuggiero, J. and Robb, J. “Divergence of the Hyperthermophilic Archaea Pyrococcus furiosus and P. horikoshii Inferred From Complete Genomic Sequences” Genetics. 1999 August. Volume 152. p. 1299-1305. <http://www.genetics.org/cgi/content/abstract/152/4/1299> 11. Liu, B., Bartlam, M., Gao, R., Zhou, W., Pang, H., Liu, Y., Feng, Y., and Rao, Z. “Crystal Structure of the Hyperthermophilic Inorganic Pyrophosphatase from the Archaeon Pyrococcus horikoshii” Biophysical Journal. 2004. Volume 86. p. 420-427. <http://www.biophysj.org/cgi/content/full/86/1/420> 12. Lokanath, N., Pampa, Kamiya, T., and Kunishima, N. “Purification, crystallization and preliminary X-ray diffraction studies of a putative UDP-N-acetyl-D-mannosamine dehydrogenase from Pyrococcus horikoshii OT3.” Acta Cryst. 2007. Volume 63. p. 412–414. <http://journals.iucr.org/f/issues/2007/05/00/bw5194/bw5194.pdf> 13. Bagautdinov, B., Matsuura, Y., Bagautdinova, S., Kunishima, N. “Crystallization and preliminary X-ray crystallographic studies of the biotin carboxyl carrier protein and biotin protein ligase complex from Pyrococcus horikoshii OT3.” 2007 April. Volume 63(4). p. 334-7. <http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=17401210&dopt=Citation> 14. Kuroita, T., Kanno, T., Kawai, A., Kawakami, B., Oka, M., Endo, Y. and Tozawa, Y. “Functional similarities of a thermostable protein-disulfide oxidoreductase identified in the archaeon Pyrococcus horikoshii to bacterial DsbA enzymes.” Extremophiles. 2007 January. Volume 11(1). p. 1431-0651. <http://www.springerlink.com/content/f4422j0063228453/>
