Pyrococcus furiosus

A Microbial Biorealm page on the genus Pyrococcus furiosus

Classification

Higher order taxa

Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; Pyrococcus

Species

Pyrococcus furiosus

Description and significance

Pyrococcus furiosus is an aquatic anaerobic hyperthermophiles archaeon first isolated in a hydrothermal vent near Vulcano Island, Italy. Its optimal growth temperature is 100 degrees C, so its enzymes are extremely thermo-stable. It is one of the first hyperthermophiles to be studied extensively by scientists, and it was found that its enzymes and proteins are highly resistant to heat shock, and radiation (6). It is also notable that some of its enzymes are tungsten dependent, a very rare element to be found in biological system (5, 18). Moreover, it is unique among its kind in that it can use a wide range of compounds as a carbon source, such as peptides and carbohydrates (14). And unlike other hyperthermophiles, it does not need elemental sulfur for growth (7).

Genome structure

P. furiosus is a single circular chromosome organism. Its genome size is approximately 1.9Mb, with 40.8% of G-C content, and 2,065 open reading frames encoding proteins, 470 operons (4). Of these 2,065 ORFs, 6% (130 ORFs) have been found to be unique to P. furiosus (1, 10). Experimental evidence has shown that it has at least two stable shuttle vectors, and some Insertion Sequence element, suggesting that it has mobile DNA element. And, at least 100 ORFs have been acquired through lateral gene transfer (12).

Cell structure and metabolism

Cell Structure

P. furiosus has flagella that are attached to one pole of the cell. It is composed of mainly one type of glycoprotein similar to bacterial flagellin, but differs in other aspects from bacterial flagella. While bacterial flagella are hollow tubes of a single flagellin growing from the tip, archeal flagella are form from many flagellin, and it’s been argued that it might grow from the root (yet to be proven). These flagella are also havw a very unique function in addition to motility. In about 5% of the cells during stationary phase, the flagella form cable like structure and allow cell to cell connection, a function very much similar to sex pilus in many bacteria. And, it also allows P. furiosus cells to attach themselves to a solid surface; along with connection to other cells, P. furiosus can live in a community that’s similar to that of a biofilm of bacteria (12).

Metabolism

Living in such an extreme environment, P. furiosus has other remarkable mechanisms to protect and proliferate itself. In a more general study of hyperthermophiles, it has been found that their enzymes are generally more rigid in structure to prevent from environmental adverse effect (23). Hyperthermophiles also have different protein properties due to adaptation of their environment. It was found that their proteins are generally denser, having a shorter surface loop length, and solvent exposed surface area (24). In yet another study, it was speculated that the pressure in its environment may help to stabilize its enzymes, raising its resistance against thermal inactivation (25). In addition to this, hyperthermophiles also have a DNA binding protein that helps to protect it from hydrolytic DNA backbone damage (29).

P. furiosus was exposed to gamma radiation in a study, and the hydroxyl radical the radiation causeds from radiolysis of water did extensive damage to the DNA backbone. But upon exposure, the level of the radA gene, whose protein function to repair DNA damage, is induced to express at high level (6). Moreover, it has ATP dependent chaperonin activity, also known as thermosomes, to help its proteins from thermal inactivation (8).

Since it is a hyperthermophile, it is actually crippling to these organisms to be at the lower to moderate range of temperature. When the temperate of a culture of P. furiosus is dropped from 95 0C to 72 0C, there was a 5 hours lag in its growth phase. During this lag phase, it is adjusting its metabolic processes to the cold environment by halting unnecessary metabolic reactions, and enhancing transcription of some enzymes needed to maintain viability. During the later stage of this cold shock response, it is adjusting to the environment, and metabolic processes that were initially halted are now returning back to the pre shock level (15). P. furiosus does not have genes to deal with heat shock like other organisms, so how it manages to survive at such extreme temperatures is a wonder. In the present of extreme heat, it does induce the formation of appropriate solutes that help to stabilize the cellular proteins against denaturation (16).

P. furiosus is very unique among its genus, for it can use both peptides and carbohydrates as its carbon source. When growing on peptide, P. furiosus needs the presence of elemental sulfur. The exact mechanism of peptide metabolism and the specific role of sulfur in it has yet been uncovered, but it is concluded that it plays a role in peptide metabolism (22). It can also use a wide range of carbohydrates, notable is the metabolism of beta linkage glucose polymers (such as cellubiose, chitin, and laminarin). Cellubiose, along with other beta linkage polymers, are taken into the cell by the ABC transport system, and are hydrolyzed by one of the 5 enzymes coding for amylase-properties proteins working on beta linkage polymers (13, 19). It also has alpha glucosidase to degrade alpha linkage sugars like maltose (27).

P. furiosus has a different glycolytic pathway, using 3 tungsten dependent enzymes, and bypasses the steps that produce NAD(P)H in the better known glycolytic pathway of eukaryotes (5), passing the electron to ferredoxins, which then passes through a hydrogenase to H2. There are four ORFs for hydrogenases in P. furiosus, each having a different affinity for H2, and the amount of ferredoxin determines the rate of activity for these hydrogenases (3). The ferredoxin in P. furiosus is quite unique in that it is also very thermostable, and has been confirmed that has a different iron-sulfur cluster than others in its genus (28). Another tungsten-containing protein in P. furiosus is suspected to have a role in aldehyde conversion, but more complete details have not been determined (17). Adding to its unique glycolytic pathway are two enzymes, glucokinase and phosphofructokinases; unlike its eukaryotic counterpart, it is ADP dependent rather than ATP dependent. It is speculated to be so because it helps the cell activity to return to normal faster since its cell has a higher concentration of ADP compare to ATP, since ADP is significantly more stable than ATP (18).

Since P. furiosus is an anaerobe, exposure to oxygen can be fatal to it. So to deal with the oxygen that it inevitably cannot avoid, it has two NADH oxidases, NOX1 and NOX2, to help it deal with oxidative stress cause by oxygen in the environment. NOX1 catalyzes the oxidation of NADH to both H2O2 and H2O (2). It is unique because it hasn’t been found in another organism that one enzyme can catalyze the formation of both products.

Ecology

Looking at the genome of P. furiosus, scientists have found a spherical protein that’s similar to a bacteriophage. The similarity is only in structure, and not in sequence. Since a virus can enter a host’s genome and remain there as part of the genome to be replicated, this possibly could have been the cause for this spherical viral like protein. But it is suggestive of a common virus ancestor, which then delineated to affect all three domain of life. (9).

In its genome, P. furiosus has up to 28 composite transposons, allowing for the DNA to be mobilized to other chromosomes, allowing genetic exchanges in this vent that may have lead to the divergence of other species in the vent (14). It’s been an old belief that genetic information was first encoded in RNA, it was only by the activity of ribonucleotide reductase (RNR) that DNA had evolved. Looking at the RNR in P. furiosus and its similarity to other RNRs, it is suggested that all RNRs came from a common ancestor (26).

Pathology

P. furiosus is not pathogenic.

Application to Biotechnology

P. furiosus have contributed greatly to biotechnology, and potentially will have many more useful contributions in the future as well. Because of the highly thermostable property of the enzymes of P. furiosus, its polymerase, known as Pfu, is widely used for Polymerase Chain Reaction. In addition to this, a mutant in the P. furiosus polymerase reduces its proof reading capability and causes more error during the replication process; this is helpful when scientists are trying to study the effect of mutations on the function of a gene, a technique known as mutagenesis (30). Another mutation in the polymerase enhances its affinity for dideoxy-nucleotide triphosphate (ddNTP), which is used for DNA sequencing, allowing for a more sufficient rate of sequencing (32). Another important contribution by P. furiosus is its amylolytic enzymes capabilities. Since P. furiosus is capable of using alpha and beta linkage carbohydrates, isolation of these enzymes are quite helpful to industrial processes (31).

Current Research

1. P. furiosus has a different glycolytic pathway that bypasses the reduction of NAD(P) to give the electron to ferredoxin and allow the formation of H2 using a membrane bound hydrogenase (MBH). Upon addition of elemental sulfur to the media, the rate of production of H2 decreases and H2S increases. This is due to the up regulation of an NADPH elemental sulfur oxidoreductase (NSR); this also involves the up regulation of a membrane bound oxidoreductase (MBX). Without the elemental sulfur, the H2 formed will be the final product of the glycolytic pathway; but since is H2 toxic to cell growth, getting rid of it is preferable. This study focuses on the role of NSR, and how it signals the positive feedback for MBX to replace the MBH and allow for reduction of elemental sulfur (7).

2. Ferritin is a 24 subunit protein that helps sequester free iron, keeping it in a soluble, nontoxic form until it is needed by the cell. This study focuses on the structure of the ferritin in 'P. furiosus, and how this structure helps protect it from heat inactivation. It is proposed that the large number of hydrogen bonds within the monomers of the protein allow it to retain its structure, this in turn helps protect the whole protein from thermal denaturation (11).

3. Being in such extreme environment, P. furiosus has mechanisms to protect itself against the environment stress. T This study elucidates the structure of a protein that plays as a heat shock regulator for the organism. his protein is a dimer, and it interacts with the minor groove to recognize the palindrome of the DNA. It blocks the expression of genes that aveh already been damaged by the heat until the appropriate precaution against heat shock have been taken to allow the gene to be repaired (20).

4. It is essential for polymerase to bind to Proliferating Cell Nuclear Antigen (PCNA) and slides along the DNA in the process of replication. It was already proven that PCNA and DNA Polymerase complex is needed for processive DNA synthesis. In this study with P. furisosus replication, it is demonstrated that the PIP box motif at the C-terminal of the polymerase is needed to load the PCNA onto the polymerase for it to continue on with replication (21).

References

1. National Center for Biotechnology Information. Genome Project. Retrieved June 05, 2007. From the National Center for Biotechnology Information Web Site, http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=287

2. Donald E. Ward1, Christopher J. Donnelly2, Michael E. Mullendore2, John van der Oost1, Willem M. de Vos1 and Edward J. Crane III (2001). “The NADH Oxidase from Pyrococcus furiosus: Implications for the protection of anaerobic hyperthermophiles against oxidative stress.” European Journal of Biochemistry. 268, 5816-5823. Retrieved June 05, 2007. From the Web Site, http://content.febsjournal.org/cgi/reprint/268/22/5816

3. Pedro J. Silva el al (2000). “Enzymes of hydrogen metabolism in Pyrococcus furiosus.” Retrieved June 05, 2007. From the European Journal of Biochemistry Web Site, http://www.blackwell-synergy.com/doi/abs/10.1046/j.1432-1327.2000.01745.x

4. Thao T. Tran et al(2006). “Operon prediction in Pyrococcus furiosus.” Retrieved June 05, 2007. From the PubMed Central WebSite, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubme did=17148478

5. S Mukund and MW Adams (1991). “The novel tungsten-iron-sulfur protein of the hyperthermophilic archaebacterium, Pyrococcus furiosus, is an aldehyde ferredoxin oxidoreductase. Evidence for its participation in a unique glycolytic pathway.” J. Biol. Chem., Vol. 266, Issue 22, 14208-14216. Retrieved June 05, 2007. From Web Site, http://www.jbc.org/cgi/content/abstract/266/22/14208

6. Ernest Williams et al (2006). “Microarray analysis of the hyperthermophilic archaeonPyrococcus furiosus exposed to gamma irradiation.” Retrieved June 05, 2007. From the Lowe’s Database Web Site, http://www.soe.ucsc.edu/%7Elowe/pubs/Lowe-pub-2006-C.pdf

7. Schut GJ, Bridger SL, Adams MW. (2000). “Insights into the Metabolism of Elemental Sulfur by the Hyperthermophilic Archaeon Pyrococcus furiosus: Characterization of a Coenzyme A- Dependent NAD(P)H Sulfur Oxidoreductase.” Retrieved June 05, 2007. From the PubMed Central WebSite, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17449625&itool=iconabstr&query_hl=5&itool=pubmed_DocSum

8. Hua-You Che et al (2007). “Expression and characterization of the chaperonin molecular machine from the hyperthermophilic archaeon Pyrococcus furiosus.” Retrieved June 05, 2007. From the Wiley InterScience Web Site, http://www3.interscience.wiley.com/cgi-bin/abstract/114211019/ABSTRACT

9. Fusamichi Akita et al (2007). “The Crystal Structure of a Virus-like Particle from the Hyperthermophilic Archaeon Pyrococcus furiosus Provides Insight into the Evolution of Viruses.” Retrieved June 05, 2007. From the Science Direct Web Site, http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4N68NPGC&_user=4429&_coverDate=05%2F18%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059602&_version=1&_urlVersion=0&_userid=4429&md5=256707182886bc854e5a4e331344b2e7

10. Farris L. Poole et al (2005). “Defining Genes in the Genome of the Hyperthermophilic Archaeon Pyrococcus furiosus: Implications for All Microbial Genomes.” Retrieved June 05, 2007. From the PubMed Central WebSite, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16237015

11. Tatur J. et al (2007). “Crystal structure of the ferritin from the hyperthermophilic archaeal anaerobe Pyrococcus furiosus.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17541801&itool=iconabstr&itool=pubmed_DocSum&query_hl=5

12. Daniela J. Näther et al (2006). “Flagella of Pyrococcus furiosus: Multifunctional Organelles, Made for Swimming, Adhesion to Various Surfaces, and Cell-Cell Contacts.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16980494

13. Han-Seung Lee et al (2006). “Transcriptional and Biochemical Analysis of Starch Metabolism in the Hyperthermophilic Archaeon Pyrococcus furiosus.” From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16513741

14. Scott D. Hamilton-Brehm et al (2005). “Metabolic and Evolutionary Relationships among Pyrococcus Species: Genetic Exchange within a Hydrothermal Vent Environment.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16237032

15. Michael V. Weinberg et al (2005). “Cold Shock of a Hyperthermophilic Archaeon: Pyrococcus furiosus Exhibits Multiple Responses to a Suboptimal Growth Temperature with a Key Role for Membrane-Bound Glycoproteins.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15601718

16. Keith R. Shockley et al (2003). “Heat Shock Response by the Hyperthermophilic Archaeon Pyrococcus furiosus.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12676722

17. Roopali Roy et al (2002). “Characterization of a Fourth Tungsten-Containing Enzyme from the Hyperthermophilic Archaeon Pyrococcus furiosus.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12446645

18. Corne! H. VERHEES et al (2002). “Biochemical adaptations of two sugar kinases from the hyperthermophilic archaeon Pyrococcus furiosus.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1222741&blobtype=pdf

19. Sonja M. Koning et al (2001). “Cellobiose Uptake in the Hyperthermophilic Archaeon Pyrococcus furiosus Is Mediated by an Inducible, High-Affinity ABC Transporter.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11489849

20. Wei Liu et al (2007). “Crystal Structure of the Archaeal Heat Shock Regulator from Pyrococcus furiosus: A Molecular Chimera Representing Eukaryal and Bacterial Features.” Abstract retrieved June 05, 2007. From the Science Direct Web Site, http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4NB99PB4&_user=4429&_coverDate=06%2F01%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059602&_version=1&_urlVersion=0&_userid=4429&md5=27d8c8674e4d630c605565a5b41c66ca

21. Tori et al (2007). “DNA polymerases BI and D, from the hyperthermophilic archaeon, Pyrococcus furiosus, both bind to PCNA with their C-terminal PIP box motifs..” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed

22. Michael Adams et al (2001). “Key Role for Sulfur in Peptide Metabolism and in Regulation of Three Hydrogenases in the Hyperthermophilic Archaeon Pyrococcus furiosus.” Retrieved June 05, 2007. From the PubMed Central Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11133967

23. Griselda Hernández et al (2000). “Millisecond time scale conformational flexibility in a hyperthermophile protein at ambient temperature.” Retrieved June 05, 2007. From the PubMed Central Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10716696#id2529138

24. Costantino Vetriani et al (1998). “Protein thermostability above 100°C: A key role for ionic interactions.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9770481

25. Summit M et al (1998). “Pressure enhances thermal stability of DNA polymerase from three thermophilic organisms.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=9783182&itool=iconabstr&query_hl=18&itool=pubmed_docsum

26. Joan Riera et al (1997). “Ribonucleotide reductase in the archaeon Pyrococcus furiosus: A critical enzyme in the evolution of DNA genomes?” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9012808

27. Karina B. Xavier et al (1999). “Maltose Metabolism in the Hyperthermophilic Archaeon Thermococcus litoralis: Purification and Characterization of Key Enzymes.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10348846

28. S Aono et al (1989). “A novel and remarkably thermostable ferredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2542225

29. M J Peak et al (1995). “Extreme resistance to thermally induced DNA backbone breaks in the hyperthermophilic archaeon Pyrococcus furiosus.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=7592404

30. Benjamin D. Biles et al (2001). “Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR.” Retrieved June 05, 2007. From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15601989

31. Sung-Jae Yang et al (2004). “Enzymatic Analysis of an Amylolytic Enzyme from the Hyperthermophilic Archaeon Pyrococcus furiosus Reveals Its Novel Catalytic Properties as both an α-Amylase and a Cyclodextrin-Hydrolyzing Enzyme.” Retrieved June 05, 2007. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15466542

32. Steven J. Evans et al (2000). “Improving dideoxynucleotide-triphosphate utilisation by the hyper-thermophilic DNA polymerase from the archaeon Pyrococcus furiosus.” From the PubMed Central Web Site, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10666444

Edited by ChauNhien Nguyen, student of Rachel Larsen and Kit Pogliano

KMG