''Sulfolobus'' is a

genus Genus (; : genera ) is a taxonomic rank above species and below family (taxonomy), family as used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In bino ...

microorganism A microorganism, or microbe, is an organism of microscopic scale, microscopic size, which may exist in its unicellular organism, single-celled form or as a Colony (biology)#Microbial colonies, colony of cells. The possible existence of unseen ...

in the

family Family (from ) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). It forms the basis for social order. Ideally, families offer predictabili ...

Sulfolobaceae Sulfolobaceae are a family of the Sulfolobales belonging to the domain Archaea. The family consists of several genera adapted to survive environmental niches with extreme temperature and low pH conditions. Ecology ''Sulfolobaceae'' species are ...

. It belongs to the kingdom

Thermoproteati Thermoproteati is a kingdom of archaea. Its synonym, "TACK", is an acronym for Thaumarchaeota (now Nitrososphaerota), Aigarchaeota, Crenarchaeota (now Thermoproteota), and Korarchaeota (now Thermoproteota), the first groups discovered. They a ...

of the

Archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...

domain A domain is a geographic area controlled by a single person or organization. Domain may also refer to: Law and human geography * Demesne, in English common law and other Medieval European contexts, lands directly managed by their holder rather ...

. ''Sulfolobus'' species grow in volcanic springs with optimal growth occurring at pH 2–3 and

temperature Temperature is a physical quantity that quantitatively expresses the attribute of hotness or coldness. Temperature is measurement, measured with a thermometer. It reflects the average kinetic energy of the vibrating and colliding atoms making ...

s of 75–80 °C, making them

acidophile Acidophiles or acidophilic organisms are those that thrive under highly acidic conditions (usually at pH 5.0 or below). These organisms can be found in different branches of the Tree of life (biology), tree of life, including Archaea, Bacteria,Bec ...

s and

thermophiles A thermophile is a type of extremophile that thrives at relatively high temperatures, between . Many thermophiles are archaea, though some of them are bacteria and fungi. Thermophilic eubacteria are suggested to have been among the earliest bacte ...

respectively. ''Sulfolobus'' cells are irregularly shaped and

flagella A flagellum (; : flagella) (Latin for 'whip' or 'scourge') is a hair-like appendage that protrudes from certain plant and animal sperm cells, from fungal spores ( zoospores), and from a wide range of microorganisms to provide motility. Many pr ...

r. Species of ''Sulfolobus'' are generally named after the location from which they were first isolated, e.g. ''Sulfolobus solfataricus'' (now recombined as ''Saccharolobus solfataricus)'' was first isolated in the

Solfatara A fumarole (or fumerole) is a vent in the surface of the Earth or another rocky planet from which hot volcanic gases and vapors are emitted, without any accompanying liquids or solids. Fumaroles are characteristic of the late stages of volcani ...

volcano. Other species can be found throughout the world in areas of volcanic or geothermal activity, such as geological formations called

mud pot A mudpot, or mud pool, is a type of acidic hot spring, or fumarole, with limited water. It usually takes the form of a pool of bubbling mud, as a result of the acid and microorganisms decomposing surrounding rock into clay and mud. Description ...

s, which are also known as ''solfatare'' (plural of solfatara).

''Sulfolobus'' as a model to study the molecular mechanisms of DNA replication

When the first Archaeal genome, ''

Methanococcus ''Methanococcus'' is a genus of coccoid methanogens of the family Methanococcaceae. They are all mesophiles, except the thermophilic '' M. thermolithotrophicus'' and the hyperthermophilic '' M. jannaschii''. The latter was discovered at the ba ...

jannaschii'', had been sequenced completely in 1996, it was found that the genes in the genome of ''Methanococcus jannaschii'' involved in DNA replication, transcription, and translation were more related to their counterparts in eukaryotes than to those in other prokaryotes. In 2001, the first genome sequence of ''Sulfolobus'', ''Sulfolobus solfataricus'' P2, was published. In P2's genome, the genes related to chromosome replication were likewise found to be more related to those in eukaryotes. These genes include DNA polymerase, primase (including two subunits), MCM, CDC6/ORC1, RPA, RPC, and

PCNA Proliferating cell nuclear antigen (PCNA) is a DNA clamp that acts as a processivity factor for DNA polymerase delta, DNA polymerase δ in eukaryotic cell (biology), cells and is essential for replication. PCNA is a homotrimer and achieves its ...

. In 2004, the origins of DNA replication of ''Sulfolobus solfataricus'' and ''Sulfolobus acidocaldarius'' were identified. It showed that both species contained two origins in their genome. This was the first time that more than a single origin of DNA replication had been shown to be used in a prokaryotic cell. The mechanism of DNA replication in archaea is evolutionary conserved, and similar to that of eukaryotes. ''Sulfolobus'' is now used as a model to study the molecular mechanisms of DNA replication in Archaea. And because the system of DNA replication in Archaea is much simpler than that in Eukaryota, it was suggested that Archaea could be used as a model to study the much more complex DNA replication in Eukaryota.

Role in biotechnology

''Sulfolobus'' proteins are of interest for biotechnology and industrial use due to their

thermostable In materials science and molecular biology, thermostability is the ability of a substance to resist irreversible change in its chemical or physical structure, often by resisting decomposition or polymerization, at a high relative temperature. Th ...

nature. One application is the creation of artificial derivatives from '' S. acidocaldarius'' proteins, named ''

affitin Affitins (commercial name Nanofitins) are artificial proteins with the ability to selectively bind antigens. They are structurally derived from the DNA binding protein Sac7d, found in ''Sulfolobus acidocaldarius'', a microorganism belonging to th ...

s''. Intracellular proteins are not necessarily stable at low pH however, as ''Sulfolobus'' species maintain a significant pH gradient across the outer membrane. ''Sulfolobales'' are metabolically dependent on sulfur:

heterotroph A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...

ic or

autotroph An autotroph is an organism that can convert Abiotic component, abiotic sources of energy into energy stored in organic compounds, which can be used by Heterotroph, other organisms. Autotrophs produce complex organic compounds (such as carbohy ...

ic, their energy comes from the

oxidation Redox ( , , reduction–oxidation or oxidation–reduction) is a type of chemical reaction in which the oxidation states of the reactants change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is ...

sulfur Sulfur ( American spelling and the preferred IUPAC name) or sulphur ( Commonwealth spelling) is a chemical element; it has symbol S and atomic number 16. It is abundant, multivalent and nonmetallic. Under normal conditions, sulfur atoms ...

and/or

cellular respiration Cellular respiration is the process of oxidizing biological fuels using an inorganic electron acceptor, such as oxygen, to drive production of adenosine triphosphate (ATP), which stores chemical energy in a biologically accessible form. Cell ...

in which sulfur acts as the final electron acceptor. For example, ''S. tokodaii'' is known to

oxidize Redox ( , , reduction–oxidation or oxidation–reduction) is a type of chemical reaction in which the oxidation states of the reactants change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is ...

hydrogen sulfide Hydrogen sulfide is a chemical compound with the formula . It is a colorless chalcogen-hydride gas, and is toxic, corrosive, and flammable. Trace amounts in ambient atmosphere have a characteristic foul odor of rotten eggs. Swedish chemist ...

sulfate The sulfate or sulphate ion is a polyatomic anion with the empirical formula . Salts, acid derivatives, and peroxides of sulfate are widely used in industry. Sulfates occur widely in everyday life. Sulfates are salts of sulfuric acid and many ...

intracellularly.

Phylogeny

The currently accepted taxonomy is based on the

List of Prokaryotic names with Standing in Nomenclature List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclatu ...

(LPSN) and

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is lo ...

(NCBI)

Genome status

The complete

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

s have been sequenced for ''S. acidocaldarius'' DSM 639 (2,225,959

nucleotides Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...

), ''S. solfataricus'' P2 (2,992,245 nucleotides), and ''S. tokodaii'' str. 7 (2,694,756 nucleotides).

Genome structure

The archaeon ''Sulfolobus solfataricus'' has a circular chromosome that consists of 2,992,245 bp. Another sequenced species, ''S. tokodaii'' has a circular chromosome as well but is slightly smaller with 2,694,756 bp. Both species lack the genes ftsZ and minD, which has been characteristic of sequenced Crenarchaeota. They also code for citrate synthase and two subunits of 2-oxoacid:ferredoxin oxidoreductase, which plays the same role as alpha-ketoglutarate dehydrogenase in the TCA (tricarboxylic/Krebs/citric acid) cycle. This indicates that ''Sulfolobus'' has a TCA cycle system similar to that found in mitochondria of eukaryotes. Other genes in the respiratory chain which partake in the production of ATP were not similar to what is found in eukaryotes. Cytochrome c is one such example that plays an important role in electron transfer to oxygen in eukaryotes. This was also found in A. pernix K1. Since this step is important for an aerobic microorganism like ''Sulfolobus'', it probably uses a different molecule for the same function or has a different pathway.

Cell structure and metabolism

''Sulfolobus'' can grow either lithoautotrophically by oxidizing sulfur, or chemoheterotrophically using sulfur to oxidize simple reduced carbon compounds. Heterotrophic growth has only been observed, however, in the presence of oxygen. The principle metabolic pathways are a glycolytic pathway, a pentose phosphate pathway, and the TCA cycle. All Archaea have lipids with ether links between the head group and side chains, making the lipids more resistant to heat and acidity than bacterial and eukaryotic ester-linked lipids. The Sulfolobales are known for unusual tetraether lipids. In Sulfolobales, the ether-linked lipids are joined covalently across the "bilayer," making tetraethers. Technically, therefore, the tetraethers form a monolayer, not a bilayer. The tetraethers help ''Sulfolobus'' species survive extreme acid as well as high temperature.

Ecology

''S. solfataricus'' has been found in different areas including

Yellowstone National Park Yellowstone National Park is a List of national parks of the United States, national park of the United States located in the northwest corner of Wyoming, with small portions extending into Montana and Idaho. It was established by the 42nd U ...

Mount St. Helens Mount St. Helens (known as Lawetlat'la to the local Cowlitz people, and Loowit or Louwala-Clough to the Klickitat) is an active stratovolcano located in Skamania County, Washington, in the Pacific Northwest region of the United States ...

Iceland Iceland is a Nordic countries, Nordic island country between the Atlantic Ocean, North Atlantic and Arctic Oceans, on the Mid-Atlantic Ridge between North America and Europe. It is culturally and politically linked with Europe and is the regi ...

Italy Italy, officially the Italian Republic, is a country in Southern Europe, Southern and Western Europe, Western Europe. It consists of Italian Peninsula, a peninsula that extends into the Mediterranean Sea, with the Alps on its northern land b ...

, and

Russia Russia, or the Russian Federation, is a country spanning Eastern Europe and North Asia. It is the list of countries and dependencies by area, largest country in the world, and extends across Time in Russia, eleven time zones, sharing Borders ...

to name a few. ''Sulfolobus'' is located almost wherever there is

volcanic activity Volcanism, vulcanism, volcanicity, or volcanic activity is the phenomenon where solids, liquids, gases, and their mixtures erupt to the surface of a solid-surface astronomical body such as a planet or a moon. It is caused by the presence of a he ...

. They thrive in environments where the temperature is about 80 °C with a pH at about 3 and sulfur present. Another species, '' S. tokodaii'', has been located in an acidic spa in Beppu Hot Springs,

Kyushu is the third-largest island of Japan's Japanese archipelago, four main islands and the most southerly of the four largest islands (i.e. excluding Okinawa Island, Okinawa and the other Ryukyu Islands, Ryukyu (''Nansei'') Ryukyu Islands, Islands ...

Japan Japan is an island country in East Asia. Located in the Pacific Ocean off the northeast coast of the Asia, Asian mainland, it is bordered on the west by the Sea of Japan and extends from the Sea of Okhotsk in the north to the East China Sea ...

. Sediments from ~90m below the seafloor on the Peruvian continental margin are dominated by intact archaeal tetraethers, and a significant fraction of the community is sedimentary archaea taxonomically linked to the crenarchaeal Sulfolobales (Sturt, ''et al.'', 2004).

DNA damage response

Exposure of ''Sulfolobus solfataricus'' or ''Sulfolobus acidocaldarius'' to the DNA damaging agents UV-irradiation, bleomycin or mitomycin C induced cellular aggregation. Other physical stressors, such as pH or temperature shift, did not induce aggregation, suggesting that induction of aggregation is caused specifically by DNA damage. Ajon et al. showed that UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency in ''S. acidocaldarius''. Recombination rates exceeded those of uninduced cultures by up to three orders of magnitude. Wood et al. also showed that UV-irradiation increased the frequency of recombination due to genetic exchange in ''S. acidocaldarius''. Frols et al. and Ajon et al. hypothesized that the UV-inducible DNA transfer process and subsequent homologous recombinational repair represents an important mechanism to maintain chromosome integrity in ''S. acidocaldarius'' and ''S. solfataricus''. This response may be a primitive form of sexual interaction, similar to the more well-studied bacterial transformation that is also associated with DNA transfer between cells leading to homologous recombinational repair of DNA damage.

The ''ups'' operon

The ''ups''

operon In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splic ...

of ''Sulfolobus'' species is highly induced by UV irradiation. The pili encoded by this operon are employed in promoting cellular aggregation, which is necessary for subsequent DNA exchange between cells, resulting in

homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in Cell (biology), cellular organi ...

. A study of the ''Sulfolobales acidocaldarius'' ''ups'' operon showed that one of the genes of the operon, ''saci-1497'', encodes an

endonuclease In molecular biology, endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain (namely DNA or RNA). Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (with regard to sequence), while man ...

III that nicks UV-damaged DNA; and another gene of the operon, ''saci-1500'', encodes a RecQ-like helicase that is able to unwind

intermediates such as

Holliday junctions A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the ju ...

. It was proposed that Saci-1497 and Saci-1500 function in an homologous recombination-based DNA repair mechanism that uses transferred DNA as a template. Thus it is thought that the ''ups'' system in combination with

provide a DNA damage response which rescues ''Sulfolobales'' from DNA damaging threats.

''Sulfolobus'' as a viral host

Lysogenic Lysogeny, or the lysogenic cycle, is one of two cycles of viral reproduction (the lytic cycle being the other). Lysogeny is characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome or formation of a cir ...

viruses infect ''Sulfolobus'' for protection. The viruses cannot survive in the extremely acidic and hot conditions that ''Sulfolobus'' lives in, and so the viruses use ''Sulfolobus'' as protection against the harsh elements. This relationship allows the virus to replicate inside the archaea without being destroyed by the environment. The Sulfolobus viruses are temperate or permanent lysogens. Permanent lysogens differ from lysogenic bacteriophages in that the host cells are not lysed after the induction of Fuselloviridae production and eventually return to the lysogenic state. They are also unique in the sense that the genes encoding the structural proteins of the virus are constantly transcribed and DNA replication appears to be induced. The viruses infecting archaea like Sulfolobus have to use a strategy to escape prolonged direct exposure to the type of environment their host lives in, which may explain some of their unique properties.

References

External links

Comparative Analysis of Sulfolobus Genomes
(at DOE's IMG system)
Sulfolobus Genome Projects
(fro
Genomes OnLine Database
{{Taxonbar, from=Q1209791 Archaea genera Thermoproteota