| Haloferax volcanii | |
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| A lab-grown culture of Haloferax volcanii imaged under an agarose pad using phase contrast microscopy. | |
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| Species: | H. volcanii |
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| Haloferax volcanii (Mullakhanbhai and Larsen, 1975) Torreblanca et al., 1986 | |
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Haloferax volcanii is a species of organism in the genus Haloferax in the Archaea.
H. volcanii is a halophilic mesophile archaeon that can be isolated from hypersaline environments such as: the Dead Sea, the Great Salt Lake, and oceanic environments with high sodium chloride concentrates. Haloferax volcanii is noteworthy because it can be cultured without much difficulty, rare for an extremophile. H. volcanii is chemoorganotrophic, metabolizing sugars as a carbon source. [2] It is primarily aerobic, but is capable of anaerobic respiration under anoxic conditions. [3] Recently an isolate of this species was studied by researchers at University of California, Berkeley, as part of a project on the survival of haloarchaea on Mars.
The genome of H. volcanii consists of a large (4 Mb), multicopy chromosome and several megaplasmids. The complete genome of the wild-type strain of H. volcanii (DS2) consists of about 4130 genes. [4]
The genome has been completely sequenced and a paper discussing it was published in 2010. [5] The molecular biology of H. volcanii has been extensively studied for the last decade in order to discover more about DNA replication, DNA repair and RNA synthesis. The archaeal proteins used in these processes are extremely similar to Eukaryotic proteins and so are studied primarily as a model system for these organisms. H. volcanii undergoes prolific horizontal gene transfer through a mechanism of "mating"- cell fusion.
Reproduction among H. volcanii occurs asexually by binary fission. This practice is similar to that of other Archaea and, indeed, that of bacteria.
Like many archaea, H. volcanii cells have no cell wall and therefore are dependent on other mechanisms, such as their S-layer and cytoskeletal proteins, for structure. [6] An individual H. volcanii archaeon can vary from 1-3 micrometers in diameter. [7] They are pleomorphic, generally transitioning from motile, elongated rod shapes to stationary, biofilm-generating disk shapes as the culture ages. [8] Additionally, biofilms generated by H. volcanii are capable of rapidly producing honeycomb patterns when exposed to changes in humidity. [9] The membranes of this organism are made of the typical ether linked membrane lipids found solely in archaea and also contain a high level of carotenoids including lycopene, which gives them their distinctive red color.
H. volcanii use a salt in method to maintain osmostasis, rather than the typical compatible solutes method seen in bacteria. This method involves the maintenance of a high degree of potassium ions in the cell to balance the sodium ions outside. For this reason, H. volcanii has a complex ion regulation system.
H. volcanii will optimally grow at 42 °C in 1.5-2.5 M NaCl and complex nutrient medium. It will still grow at 37 °C, but still requires the concentrated NaCl and complex medium. [4]
Due to the salt in method cytoplasmic proteins are structured to fold in the presence of high ionic concentrations. As such, they typically have a large number of charged residues on the exterior section of the protein and very hydrophobic residues forming a core. This structure considerably increases their stability in saline and even high temperature environments but comes at some loss of processivity compared to bacterial homologs.
H. volcanii respire as their sole source of ATP, unlike several other halobateriacae, such as Halobacterium salinarum they are incapable of photophosphorylation as they lack the necessary bacteriorhodopsin.
Isolates of H. volcanii are commonly found in high-salinity aquatic environments, such as the Dead Sea. Their precise role in the ecosystem is uncertain, but the carbohydrates contained within these organisms potentially serve many practical purposes. Because of their ability to maintain homeostasis in spite of the salt around them, H. volcanii could be an important player in advancements in biotechnology. As it is likely that H. volcanii and comparable species are ranked among the earliest living organisms, they also provide information related to genetics and evolution. [10]
The Dead Sea contains a very high concentration of sodium, magnesium, and calcium salts. This combination makes the sea an ideal environment for extremophiles such as H.volcanii. [11] The Dead Sea has a diverse community of microorganisms, though the field tests completed by Kaplan and Friedman reported that H.volcanii had the largest numerical presence within the community. [12] It is common to find higher numbers of the halophile during the summer, as the Dead Sea is much warmer, averaging around 37 degrees Celsius, and thus more conducive to bacterial blooms. [13] Unfortunately, the Dead Sea is becoming less hospitable to extremophiles such as H. volcanii due to increasing salinity, credited to both natural factors and human activities. As the predominant environment for Haloferax volcanii, the change in salinity places the species at risk.
In prokaryotes the DNA genome is organized in a dynamic structure, the nucleoid, which is embedded in the cytoplasm. Exposure of Haloferax volcanii to stresses that damage the DNA cause compaction and reorganization of the nucleoid. [14] Compaction depends on the Mre11-Rad50 protein complex that is employed in the homologous recombinational repair of DNA double-strand breaks. Delmas et al. [14] proposed that nucleoid compaction is part of a DNA damage response that accelerates cell recovery by helping DNA repair proteins to locate targets, and by facilitating the search for intact DNA sequences during homologous recombination.
It has been shown that H. volcanii, can undergo a process of genetic exchange by mixing cells together on a solid, nitrocellulose membrane. The process of transduction and transformation were ruled out, leaving conjugation as a potential transfer mechanism. This mechanism is thought to be novel from other known forms, as genetic exchange does not seem to be unidirectional like in classic forms of conjugation of other prokaryotic systems. [15]
Prolonged contact between cells is required as cells grown in liquid media, while being agitated, show no genetic transfer. [15] Electron microscopy experiments have captured images of H. volcanii cells attached to each other via multiple cytoplasmic bridge-like structures [16] and it is thought that this is the apparent method of genetic exchange. The protein machinery directly involved in the formation of these bridges and transfer of DNA is yet to be discovered though a study publishing RNAseq data hints at various proteins involved. [17] Others have also shown that messing with environmental salt concentrations, [18] global glycosylation, [18] and cell surface lipidation [19] alter the rate of the genetic transfer.
This archaeal DNA conjugation system has been shown to even work in an interspecies manner as H. volcanii and the closely related species H. mediterranei are able to exchange genetic information by this process at a similar level to intraspecies exchange. [20] Unless selecting for the need to recombine the exchanging chromosomes, recombination is not required for survival of the exchanging cells. This can leads to the formation of hybrid cells containing 2 distinct chromosomes. [20]
CRISPR may also be playing a role in the regulation of this genetic transfer as cells are shown to acquire new spacers into their CRISPR arrays during this process. [21]
The conditions Haloferax volcanii survives in, high salinity and high radiation, are very similar to the conditions found on Mars' surface. Consequently, the organism is currently being used to test the survivability of earth native extremophiles on Mars. Advances in this field could lead to a greater understanding of the possibility and timeline of extraterrestrial life. [22]
A halophile is an extremophile that thrives in high salt concentrations. In chemical terms, halophile refers to a Lewis acidic species that has some ability to extract halides from other chemical species.
A thermoacidophile is an extremophilic microorganism that is both thermophilic and acidophilic; i.e., it can grow under conditions of high temperature and low pH. The large majority of thermoacidophiles are archaea or bacteria, though occasional eukaryotic examples have been reported. Thermoacidophiles can be found in hot springs and solfataric environments, within deep sea vents, or in other environments of geothermal activity. They also occur in polluted environments, such as in acid mine drainage.
Halobacterium is a genus in the family Halobacteriaceae.
Microbial genetics is a subject area within microbiology and genetic engineering. Microbial genetics studies microorganisms for different purposes. The microorganisms that are observed are bacteria, and archaea. Some fungi and protozoa are also subjects used to study in this field. The studies of microorganisms involve studies of genotype and expression system. Genotypes are the inherited compositions of an organism. Genetic Engineering is a field of work and study within microbial genetics. The usage of recombinant DNA technology is a process of this work. The process involves creating recombinant DNA molecules through manipulating a DNA sequence. That DNA created is then in contact with a host organism. Cloning is also an example of genetic engineering.
Halobacterium salinarum, formerly known as Halobacterium cutirubrum or Halobacterium halobium, is an extremely halophilic marine obligate aerobic archaeon. Despite its name, this is not a bacterium, but a member of the domain Archaea. It is found in salted fish, hides, hypersaline lakes, and salterns. As these salterns reach the minimum salinity limits for extreme halophiles, their waters become purple or reddish color due to the high densities of halophilic Archaea. H. salinarum has also been found in high-salt food such as salt pork, marine fish, and sausages. The ability of H. salinarum to survive at such high salt concentrations has led to its classification as an extremophile.
In taxonomy, Thermococcus is a genus of thermophilic Archaea in the family the Thermococcaceae.
In taxonomy, Haloferax is a genus of halobacteria in the order Haloferacaceae.
In taxonomy, Natrialba is a genus of the Natrialbaceae. The genus consists of many diverse species that can survive extreme environmental niches, especially they are capable to live in the waters saturated or nearly saturated with salt (halophiles). They have certain adaptations to live within their salty environments. For example, their cellular machinery is adapted to high salt concentrations by having charged amino acids on their surfaces, allowing the cell to keep its water molecules around these components. The osmotic pressure and these amino acids help to control the amount of salt within the cell.
Halocins are bacteriocins produced by halophilic Archaea and a type of archaeocin.
A prokaryote is a single-cell organism whose cell lacks a nucleus and other membrane-bound organelles. The word prokaryote comes from the Ancient Greek πρό 'before' and κάρυον 'nut, kernel'. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. But in the three-domain system, based upon molecular analysis, prokaryotes are divided into two domains: Bacteria and Archaea. Organisms with nuclei are placed in a third domain, Eukaryota.
Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.
The archaellum is a unique structure on the cell surface of many archaea that allows for swimming motility. The archaellum consists of a rigid helical filament that is attached to the cell membrane by a molecular motor. This molecular motor – composed of cytosolic, membrane, and pseudo-periplasmic proteins – is responsible for the assembly of the filament and, once assembled, for its rotation. The rotation of the filament propels archaeal cells in liquid medium, in a manner similar to the propeller of a boat. The bacterial analog of the archaellum is the flagellum, which is also responsible for their swimming motility and can also be compared to a rotating corkscrew. Although the movement of archaella and flagella is sometimes described as "whip-like", this is incorrect, as only cilia from Eukaryotes move in this manner. Indeed, even "flagellum" is a misnomer, as bacterial flagella also work as propeller-like structures.
Exosortase refers to a family of integral membrane proteins that occur in Gram-negative bacteria that recognizes and cleaves the carboxyl-terminal sorting signal PEP-CTERM. The name derives from a predicted role analogous to sortase, despite the lack of any detectable sequence homology, and a strong association of exosortase genes with exopolysaccharide or extracellular polymeric substance biosynthesis loci. Many archaea have an archaeosortase, homologous to exosortases rather than to sortases. Archaeosortase A recognizes the signal PGF-CTERM, found at the C-terminus of some archaeal S-layer proteins. Following processing by archaeosortase A, the PGF-CTERM region is gone, and a prenyl-derived lipid anchor is present at the C-terminus instead.
An archaeosortase is a protein that occurs in the cell membranes of some archaea. Archaeosortases recognize and remove carboxyl-terminal protein sorting signals about 25 amino acids long from secreted proteins. A genome that encodes one archaeosortase may encode over fifty target proteins. The best characterized archaeosortase target is the Haloferax volcanii S-layer glycoprotein, an extensively modified protein with O-linked glycosylations, N-linked glycosylations, and a large prenyl-derived lipid modification toward the C-terminus. Knockout of the archaeosortase A (artA) gene, or permutation of the motif Pro-Gly-Phe (PGF) to Pro-Phe-Gly in the S-layer glycoprotein, blocks attachment of the lipid moiety as well as blocking removal of the PGF-CTERM protein-sorting domain. Thus archaeosortase appears to be a transpeptidase, like sortase, rather than a simple protease.
Halobacterium noricense is a halophilic, rod-shaped microorganism that thrives in environments with salt levels near saturation. Despite the implication of the name, Halobacterium is actually a genus of archaea, not bacteria. H. noricense can be isolated from environments with high salinity such as the Dead Sea and the Great Salt Lake in Utah. Members of the Halobacterium genus are excellent model organisms for DNA replication and transcription due to the stability of their proteins and polymerases when exposed to high temperatures. To be classified in the genus Halobacterium, a microorganism must exhibit a membrane composition consisting of ether-linked phosphoglycerides and glycolipids.
Saccharolobus solfataricus is a species of thermophilic archaeon. It was transferred from the genus Sulfolobus to the new genus Saccharolobus with the description of Saccharolobus caldissimus in 2018.
Shiladitya DasSarma is a molecular biologist well-known for contributions to the biology of halophilic and extremophilic microorganisms. He is a Professor in the University of Maryland Baltimore. He earned a PhD degree in biochemistry from the Massachusetts Institute of Technology and a BS degree in chemistry from Indiana University Bloomington. Prior to taking a faculty position, he conducted research at the Massachusetts General Hospital, Harvard Medical School, and Pasteur Institute, Paris.
Haloferax mediterranei is a species of archaea in the family Haloferacaceae.
A protein-sorting transpeptidase is an enzyme, such as the sortase SrtA of Staphylococcus aureus, that cleaves one or more target proteins produced by the same cell, as part of a specialized pathway of protein targeting. The typical prokaryotic protein-sorting transpeptidase is characterized as a protease, but does not simply hydrolyze a peptide bond. Instead, the larger, N-terminal portion of the cleaved polypeptide is transferred onto another molecule, such as a precursor of the peptidoglycan cell wall in Gram-positive bacteria.
Archaea, one of the three domains of life, are a highly diverse group of prokaryotes that include a number of extremophiles. One of these extremophiles has given rise to a highly complex new appendage known as the hamus. In contrast to the well-studied prokaryotic appendages pili and fimbriae, much is yet to be discovered about archaeal appendages such as hami. Appendages serve multiple functions for cells and are often involved in attachment, horizontal conjugation, and movement. The unique appendage was discovered at the same time as the unique community of archaea that produces them. Research into the structure of hami suggests their main function aids in attachment and biofilm formation. This is accomplished due to their evenly placed prickles, helical structure, and barbed end. These appendages are heat and acid resistant, aiding in the cell's ability to live in extreme environments.