Picrophilus torridus

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A Microbial Biorealm page on the genus Picrophilus torridus

Contents

Classification

Higher order taxa

Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmatales; Picrophilaceae; Picrophilus

Species

NCBI: Taxonomy

Picrophilus torridus

Description and Significance

Picrophilaceae are the most acidophilic organism known that are able to grow at low pH values. Picrophilus torridus belong to one of the two archaela subdomains, Euryarchaea, and is a member of the genus Picrophilus. Picrophilus torridus has a circular cell shape with 1.5mm in diameter. Picrophilus torridus is known to be one of the most thermoacidophilic organisms because it is able to grow around the pH value of zero and up to 65 degrees C in temperature. The archaea has the smallest genome among non-parasitic free-living organisms. Among the thermoacidophiles, Picrophilus torridus is one of the highest coding density. (1) Picrophilus torridus has high proton concentration surrounding it, which supports it in its transport processes.

Picrophilus torridus along with picrophilus oshimae was first isolated from a dry solfataric field located in Hokkaido, northern Japan. (2) Picrophilus torridus was able to adapt to conditions such as those in 1.2 M sulfuric acid. (1) Since Picrophilus grow in extreme acidic habitat, it makes them model organisms to study thermoacidophilic adaptation.

Genome structure

The genome sequence of P. torridus has become available and has allowed further understanding of thermoacidophiles. The genome of Picrophilus torridus includes a large single circular chromosome of 1,545,900 bp. The archaea represents one of the highest coding density in the genomes of the thermoacidophile group, since a total of 92% of the sequence is coding (1). 12% of all genes in the P. torridus genome play a role in transport. (4) This shows that P. torridus is well depended on transporters for its survival.

At first, comparative genomic analysis revealed that there are significance similarities between the genomes of P. torridus, Thermoplasma acidophilum, and Sulfolobus solfataricus because they share nearly the same number of homologs. However, it was later found that the DNA dependent RNA polymerase of P. torridus is identical in subunit composition; its amino acid sequence is highly similar to the RNAPs of Ferroplasma acidarmanus and T. acidophilum. Thus resulted in the phylogenetic distance of these two organisms in the 16S-rRNA tree. (1)

Picrophilus cells contain unusual low pH of 4.6 intracellular compared to other thermoacidphiles which pH values lie close to neutral (1). Thus the extracellular along with the intracellular proteins together presents acid stability. This conclusion will allow further studies for the reason of how other genomes are able to withhold their acid stability.

Cell structure

One of the major reasons why P. torridus is able to adapt to the acidic environment is due to the nature of its cell wall and membrane. Picrophilus torridus has a typical archaeal cell membrane that consists mainly of polar ether lipids and has a S-layer. (4) The membrane is acid stable and shows particularly low proton permeability at acidic pH; the essential role of the cell membrane in the acidophilic adaptation. At neutral, the lipids are not able to assemble into liposomes, suggesting that the loss of cell integrity above pH 4.0 is caused by an impairment of this barrier function. P. torridus cell envelope is in the form of an S-layer. (4) Reasons for the acid resistance of the cell wall by the genome sequence still remain a mystery.

P. torridus has primary transporter (ABC permeases that use the energy of ATP hydrolysis) and secondary transporters that use the transmembrane potential to drive the transport. Secondary transporters in P. torridus use proton instead of Na +. Transport systems have been found for sugars and peptides, inorganic elements, as well as drug export, which are probably involved in detoxification of the cell. (4) A total of 21 transporters are predicted to be involved in drug export. (1)

Metabolism

Picrophilus Torridus can use many type of sugars as their energy source, as well as propionate. P. torridus degrade glucose through the nonphosphorylative Entner-Doudoroff pathway and produce pyruvate as its product. P. torridus appears to contain a complete set of genes for the oxidative tricarboxylic acid cycle. (1)

P. torridus has extracellular acid proteases that will degrade proteins and peptide. There are four ATP-binding cassette (ABC) transporters for the uptake of di- and oligopeptides, which can be further degraded to free amino acid by tricorn peptidase, two tricorn cofactors, an acylaminoacyl peptidase, a proline dipeptidase, and a metallo-carboxypeptidase. (1)

Biosynthetic pathways for all 20 amino acids were detected in the P. torridus genome. Amino acids are the major source of carbon and energy for Picrophilus. Genome analysis of P. torridus revealed that this organism possess particular genes and pathways for the degradation of apartate, glutamate, serine, arginine, histidine, glycine, threonine, and the aromatic amino acids phenylalanine and tyrosine. (1)

Ecology and Pathology

Many Archea live under conditions that challenge the physico-chemical limits to life: low or high temperature, extremes of pH, elevated pressure and high salt concentration. (4) One of the species that fall under the domain Archea is Picrophilus torridus, which are found in high temperature, very acidic, and solfataric environment. P. torridus grows optimally at about 60 degree Celsius and pH values between 0 and 2. P. torridus has the membrane and cell structure that can withstand the harsh environment.

Archea have been isolated from the human colon, vagina, and oral cavity, but have not been established as causes of human disease. One of the studies has revealed a relationship between the severity of periodontal disease and the relative abundance of archaeal small subunit ribosomal RNA genes (SSU rDNA) in the subgingival crevice by using quantitative PCR. (7) However, P. torridus is not known as a pathogen.


Application to Biotechnology

Picrophilus torridus is the most thermoacidophilic organism known. It inhabits solfataric environments with a low pH value below one 1 and a temperature of about 60 degrees C. The low pH adapted enzyme of P. torridus will most likely be found useful for biotechnological applications that are required for acidic conditions. (5) P. torridus evolved membrane with low proton permeability and special lipid composition together with efficient transport mechanisms to maintain the internal pH at values compatible with biomedical functions. P. torridus uses the internal high proton concentration to power a large number of solute secondary transporters. (5)

Current Research

The researcher are interested in P. torridus stunning abilities to thrive in low pH condition and high temperature. Most of the research done on P. torridus is about its properties and metabolic pathway that allow P. torridus to survive in extreme condition. P. torridus can utilizes glucose as a growth substrate as well as many other sugars. Recent analysis of glucose degradation pathway revealed that in P. torridus a nonphosphorylative version of the Entner-Doudoroff (ED) pathway is operative. (3)

The key enzyme, glycerate kinease (GCK), for nonphosphorylative Entner-Doudoroff pathway in P. torridus is characterized and its encoding genes have been identified by MALDI-TOF analysis. GCK catalyzed the ATP-dependent phosphorylation of glycerate to 2-phosphoglycerate and ADP. The apparent molecular mass of GCK was determined by gelfiltration on a Superdex 200 HiLoad 16/60 column at ambient temperature. (6)


References

Futterer, O., Angelov, A., Liesegang, H., Gottschalk, G., Schleper, C., Schepers, B., Dock, C., Antranikian, G., and Liebl W. "Genome sequence of Picrophilus torridus and its implications for life around pH 0." June 15, 2004, PNAS Vol. 101, No. 24, p. 9091-9096.

Schleper, C., Puehler, G., Holz, I., Gambacorta, A., Janekovic, D., Santarius, U., Klenk, H.P., and Zillig W. "Picrophilus gen. nov., fam. nov.: a novel aerobic, heterotrophic, thermoacidophilic genus and family comprising archaea capable of growth around pH 0." J. Bacteriol. (December, 1995) Vol.177, No. 24, p. 7050-7059.

Reher, M., Schonheit, P. “Glyceraldehyde dehydrogenases from the thermoacidophilic euryarchaeota Picrophilus forridus and Thermoplasma acidophilum, key enzymes of the non-phosporylative Entner-Doudoroff pathway constitute a novel enzyme family within the aldehyde dehydrogenase superfamily”. FEBS Lett 580. 2006. p. 1198-1204.

Ciaramella, M., Napoli, A., and Rossi, M. “Another extreme genome: how to live at pH 0". Trends in Microbiology. December 10, 2004. Volume 13, Issue 2. p. 49-51.

Podar, M., Reysenbach, A. “New opportunities revealed by biotechnological explorations of extremeophiles”. Current Opinion in Biotechnology. May 15, 2006. Volume 17, Issue 3. p. 250-255.

Reher, M., Bott, M., Schonheit, P. “Characterization of glycerate kinage (2-phosphoglycerate forming), a key enzyme of the nonphosphorylative Entner-Doudoroff pathway, from the thermoacidophilic euryarchaeon Picrophilus torridus” FEMS Microbiol Lett 259. 2006. p. 113-119.

Lepp, P., Brinig, M., Ouverney, C., Palm, K., Armitago, G., Relman, D. “Methanogenic Archaea and human periodontal disease”. Proc Natl Acad Sci U.S.A. April 20, 2004. Volume 101, Issue 16. p. 6176-6181.


Edited by Parry Yap, student of Rachel Larsen

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