Halobacterium salinarum
Encyclopedia
Halobacterium salinarum is an extremely halophilic
marine
gram-negative
obligate aerobic archaeon
. Despite its name, this microorganism is not a bacterium
, but rather a member of the Kingdom Archaea. It is found in salted fish, hides
, hypersaline lakes, and saltern
s. 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
.
These organisms are classified as gram-negative, as they have no cell wall. The membrane consists of a single lipid bilayer surrounded by an S-layer. The S-layer
is made of a cell-surface glycoprotein
, which accounts for approximately 50% of the cell surface proteins. These proteins form a lattice in the membrane. Sulfate residues are abundant on the glycan chains of the glycoprotein, giving it a negative charge. The negative charge is believed to stabilize the lattice in high-salt conditions.
Amino acid
s are the main source of chemical energy for H. salinarum, particularly arginine
and aspartate, though they are able to metabolize other amino acids, as well. H. salinarum have been reported to not be able to grow on sugars, and therefore need to encode enzymes capable of performing gluconeogenesis
to create sugars.
) to reduce osmotic stress. Potassium levels are not at equilibrium with the environment, so H. salinarum expresses multiple active transport
ers which pump potassium into the cell.
At extremely high salt concentrations protein precipitation
will occur. To prevent the salting out of proteins, H. salinarum encodes mainly acidic proteins. The average isoelectric point
of H. salinarum proteins is 4.9. These highly acidic proteins are overwhelmingly negative in charge and are able to remain in solution even at high salt concentrations.
, it is able to survive in low-oxygen conditions by utilizing light-energy. H. salinarum express the membrane protein bacteriorhodopsin
which acts as a light-driven proton pump. It consists of two parts, the 7-transmembrane protein, bacterioopsin, and the light-sensitive cofactor, retinal
. Upon absorption of a photon
, retinal changes conformation, causing a conformational change in the bacterioopsin protein which drives proton transport.The proton gradient which is formed can then be used to generate chemical energy by ATP synthase
.
To obtain more oxygen H. salinarum produce gas vesicles, which allow them to float to the surface where oxygen levels are higher and more light is available. These vesicles are complex structures made of proteins encoded by at least 14 genes. Gas vesicles were first discovered in H. salinarum in 1967.
radiation. To compensate, they have evolved a sophisticated DNA repair
mechanism. The genome encodes DNA repair enzymes homologous to those in both bacteria and eukaryotes. This allows H. salinarum to repair damage to DNA faster and more efficiently than other organisms and allows them to be much more UV tolerant.
H. salinarum is responsible for the bright pink or red appearance of the Dead Sea and other bodies of salt water. This red color is due primarily to the presence of bacterioruberin, a 50 carbon carotenoid
pigment present within the membrane of H. salinarum. The primary role of bacterioruberin in the cell is to protect against DNA damage incurred by UV light. This protection is not, however, due to the ability of bacterioruberin to absorb UV light. Bacterioruberin protects the DNA by acting as an antioxidant
, rather than directly blocking UV light. It is able to protect the cell from reactive oxygen species
produced from exposure to UV by acting as a target. The bacterioruberin radical
produced is less reactive than the initial radical, and will likely react with another radical, resulting in termination of the radical chain reaction.
of the genome increases stability in extreme environments.
Whole proteome
comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis
and other bacteria.
and serves as an excellent model system. Methods for gene replacement and systematic knockout
have been developed, so H. salinarum is an ideal candidate for the study of archaeal genetics and functional genomics.
Scientists have previously recovered similar genetic material from the Michigan Basin
, the same region where the latest discovery was made. But that DNA, discovered in a salt-cured buffalo hide in the 1930s, was so similar to that of modern microbes that many scientists believed the samples had been contaminated. The curing salt had been derived from a mine in Saskatchewan
, the site of the most recent sample described by Jong Soo Park of Dalhousie University
in Halifax, NS, Canada.
Russell Vreeland of Ancient Biomaterials Institute of West Chester University in Pennsylvania
, USA, performed an analysis of all known halopathic bacteria, which yielded the finding that Park's bacteria contained six segments of DNA
never seen before in the halopaths. Vreeland also tracked down the buffalo skin and determined that the salt came from the same mine as Park's sample. He has also discovered an even older halopath estimated at 250 million years old in New Mexico
.
Halophile
Halophiles are extremophile organisms that thrive in environments with very high concentrations of salt. The name comes from the Greek for "salt-loving". While the term is perhaps most often applied to some halophiles classified into the Archaea domain, there are also bacterial halophiles and some...
marine
Ocean
An ocean is a major body of saline water, and a principal component of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas.More than half of this area is over 3,000...
gram-negative
Gram-negative
Gram-negative bacteria are bacteria that do not retain crystal violet dye in the Gram staining protocol. In a Gram stain test, a counterstain is added after the crystal violet, coloring all Gram-negative bacteria with a red or pink color...
obligate aerobic archaeon
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
. Despite its name, this microorganism is not a bacterium
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
, but rather a member of the Kingdom Archaea. It is found in salted fish, hides
Hides
A hide is an animal skin treated for human use. Hides include leather from cattle and other livestock animals, alligator skins, snake skins for shoes and fashion accessories and furs from wild cats, mink and bears. In some areas, leather is produced on a domestic or small industrial scale, but most...
, hypersaline lakes, and saltern
Saltern
Saltern is a word with a number of differing meanings. In English archaeology, a saltern is an area used for salt making, especially in the East Anglian fenlands....
s. 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
Salt pork
Salt pork or white bacon is salt-cured pork. It is prepared from one of three primal cuts: pork side, pork belly, or fatback. Depending on the cut, respectively, salt pork may be lean, streaky or entirely fatty. Made from the same cuts as bacon, salt pork resembles uncut slab bacon, but is...
, marine fish, and sausages. The ability of H. salinarum to survive at such high salt concentrations has led to its classification as an extremophile
Extremophile
An extremophile is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles...
.
Cell Morphology and Metabolism
Halobacteria are single-celled, rod-shaped microorganisms that are among the most ancient forms of life and appeared on earth billions of years ago.These organisms are classified as gram-negative, as they have no cell wall. The membrane consists of a single lipid bilayer surrounded by an S-layer. The S-layer
S-layer
An S-layer is a part of the cell envelope commonly found in bacteria, as well as among archaea.It consists of a monomolecular layer composed of identical proteins or glycoproteins. This two-dimensional structure is built via self-assembly and encloses the whole cell surface. Thus, the S-layer...
is made of a cell-surface glycoprotein
Glycoprotein
Glycoproteins are proteins that contain oligosaccharide chains covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycosylation. In proteins that have segments extending...
, which accounts for approximately 50% of the cell surface proteins. These proteins form a lattice in the membrane. Sulfate residues are abundant on the glycan chains of the glycoprotein, giving it a negative charge. The negative charge is believed to stabilize the lattice in high-salt conditions.
Amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
s are the main source of chemical energy for H. salinarum, particularly arginine
Arginine
Arginine is an α-amino acid. The L-form is one of the 20 most common natural amino acids. At the level of molecular genetics, in the structure of the messenger ribonucleic acid mRNA, CGU, CGC, CGA, CGG, AGA, and AGG, are the triplets of nucleotide bases or codons that codify for arginine during...
and aspartate, though they are able to metabolize other amino acids, as well. H. salinarum have been reported to not be able to grow on sugars, and therefore need to encode enzymes capable of performing gluconeogenesis
Gluconeogenesis
Gluconeogenesis is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids....
to create sugars.
High salt
To survive in extremely salty environments, this archaeon—as with other halophilic Archaeal species—utilizes compatible solutes (in particular potassium chloridePotassium chloride
The chemical compound potassium chloride is a metal halide salt composed of potassium and chlorine. In its pure state, it is odorless and has a white or colorless vitreous crystal appearance, with a crystal structure that cleaves easily in three directions. Potassium chloride crystals are...
) to reduce osmotic stress. Potassium levels are not at equilibrium with the environment, so H. salinarum expresses multiple active transport
Active transport
Active transport is the movement of a substance against its concentration gradient . In all cells, this is usually concerned with accumulating high concentrations of molecules that the cell needs, such as ions, glucose, and amino acids. If the process uses chemical energy, such as from adenosine...
ers which pump potassium into the cell.
At extremely high salt concentrations protein precipitation
Protein precipitation
Precipitation is widely used in downstream processing of biological products, such as proteins. This unit operation serves to concentrate and fractionate the target product from various contaminants. For example, in the biotechnology industry protein precipitation is used to eliminate contaminants...
will occur. To prevent the salting out of proteins, H. salinarum encodes mainly acidic proteins. The average isoelectric point
Isoelectric point
The isoelectric point , sometimes abbreviated to IEP, is the pH at which a particular molecule or surface carries no net electrical charge....
of H. salinarum proteins is 4.9. These highly acidic proteins are overwhelmingly negative in charge and are able to remain in solution even at high salt concentrations.
Low oxygen
H. salinarum can grow to such densities in salt ponds that oxygen is quickly depleted. Though it is an obligate aerobeObligate aerobe
An obligate aerobe is an aerobic organism that requires oxygen to grow. Through cellular respiration, these organisms use oxygen to oxidize substances, like sugars or fats, in order to obtain energy. During respiration, they use oxygen as the terminal electron acceptor...
, it is able to survive in low-oxygen conditions by utilizing light-energy. H. salinarum express the membrane protein bacteriorhodopsin
Bacteriorhodopsin
Bacteriorhodopsin is a protein used by Archaea, the most notable one being Halobacteria. It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell...
which acts as a light-driven proton pump. It consists of two parts, the 7-transmembrane protein, bacterioopsin, and the light-sensitive cofactor, retinal
Retinal
Retinal, also called retinaldehyde or vitamin A aldehyde, is one of the many forms of vitamin A . Retinal is a polyene chromophore, and bound to proteins called opsins, is the chemical basis of animal vision...
. Upon absorption of a photon
Photon
In physics, a photon is an elementary particle, the quantum of the electromagnetic interaction and the basic unit of light and all other forms of electromagnetic radiation. It is also the force carrier for the electromagnetic force...
, retinal changes conformation, causing a conformational change in the bacterioopsin protein which drives proton transport.The proton gradient which is formed can then be used to generate chemical energy by ATP synthase
ATP synthase
right|thumb|300px|Molecular model of ATP synthase by X-ray diffraction methodATP synthase is an important enzyme that provides energy for the cell to use through the synthesis of adenosine triphosphate . ATP is the most commonly used "energy currency" of cells from most organisms...
.
To obtain more oxygen H. salinarum produce gas vesicles, which allow them to float to the surface where oxygen levels are higher and more light is available. These vesicles are complex structures made of proteins encoded by at least 14 genes. Gas vesicles were first discovered in H. salinarum in 1967.
UV protection
There is little protection from the sun in salt ponds, so H. salinarum are often exposed to high amounts of UVUltraviolet
Ultraviolet light is electromagnetic radiation with a wavelength shorter than that of visible light, but longer than X-rays, in the range 10 nm to 400 nm, and energies from 3 eV to 124 eV...
radiation. To compensate, they have evolved a sophisticated DNA repair
DNA repair
DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...
mechanism. The genome encodes DNA repair enzymes homologous to those in both bacteria and eukaryotes. This allows H. salinarum to repair damage to DNA faster and more efficiently than other organisms and allows them to be much more UV tolerant.
H. salinarum is responsible for the bright pink or red appearance of the Dead Sea and other bodies of salt water. This red color is due primarily to the presence of bacterioruberin, a 50 carbon carotenoid
Carotenoid
Carotenoids are tetraterpenoid organic pigments that are naturally occurring in the chloroplasts and chromoplasts of plants and some other photosynthetic organisms like algae, some bacteria, and some types of fungus. Carotenoids can be synthesized fats and other basic organic metabolic building...
pigment present within the membrane of H. salinarum. The primary role of bacterioruberin in the cell is to protect against DNA damage incurred by UV light. This protection is not, however, due to the ability of bacterioruberin to absorb UV light. Bacterioruberin protects the DNA by acting as an antioxidant
Antioxidant
An antioxidant is a molecule capable of inhibiting the oxidation of other molecules. Oxidation is a chemical reaction that transfers electrons or hydrogen from a substance to an oxidizing agent. Oxidation reactions can produce free radicals. In turn, these radicals can start chain reactions. When...
, rather than directly blocking UV light. It is able to protect the cell from reactive oxygen species
Reactive oxygen species
Reactive oxygen species are chemically reactive molecules containing oxygen. Examples include oxygen ions and peroxides. Reactive oxygen species are highly reactive due to the presence of unpaired valence shell electrons....
produced from exposure to UV by acting as a target. The bacterioruberin radical
Radical (chemistry)
Radicals are atoms, molecules, or ions with unpaired electrons on an open shell configuration. Free radicals may have positive, negative, or zero charge...
produced is less reactive than the initial radical, and will likely react with another radical, resulting in termination of the radical chain reaction.
Genome
Whole genome sequences are available for two strains of H. salinarum, NRC-1 and R1. The Halobacterium sp. NRC-1 genome consists of 2,571,010 base pairs on one large chromosome and two mini-chromosomes. The genome encodes 2,360 predicted proteins. The large chromosome is very G-C rich (68%). High GC-contentGC-content
In molecular biology and genetics, GC-content is the percentage of nitrogenous bases on a DNA molecule that are either guanine or cytosine . This may refer to a specific fragment of DNA or RNA, or that of the whole genome...
of the genome increases stability in extreme environments.
Whole proteome
Proteome
The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome.The term has been...
comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis
Bacillus subtilis
Bacillus subtilis, known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium commonly found in soil. A member of the genus Bacillus, B. subtilis is rod-shaped, and has the ability to form a tough, protective endospore, allowing the organism to tolerate...
and other bacteria.
H. salinarum as a model organism
H. salinarum is as easy to culture as E. coliEscherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
and serves as an excellent model system. Methods for gene replacement and systematic knockout
Gene knockout
A gene knockout is a genetic technique in which one of an organism's genes is made inoperative . Also known as knockout organisms or simply knockouts, they are used in learning about a gene that has been sequenced, but which has an unknown or incompletely known function...
have been developed, so H. salinarum is an ideal candidate for the study of archaeal genetics and functional genomics.
H. salinarum for hydrogen production
Hydrogen production using H. salinarium coupled to a hydrogenase donor like E. coli are reported in literature.Oldest DNA Ever Recovered
A sample of a close genetic relative of H. salinarum encapsulated in salt has allowed for the recovery of DNA fragments estimated at 121 million years old. Oddly, the material had been also recovered earlier, but it proved to be so similar to the modern descendants that scientists had believed the earlier samples were contaminated.Scientists have previously recovered similar genetic material from the Michigan Basin
Michigan Basin
The Michigan Basin is a geologic basin centered on the Lower Peninsula of the US state of Michigan. The feature is represented by a nearly circular pattern of geologic sedimentary strata in the area with a nearly uniform structural dip toward the center of the peninsula.The basin is centered in...
, the same region where the latest discovery was made. But that DNA, discovered in a salt-cured buffalo hide in the 1930s, was so similar to that of modern microbes that many scientists believed the samples had been contaminated. The curing salt had been derived from a mine in Saskatchewan
Saskatchewan
Saskatchewan is a prairie province in Canada, which has an area of . Saskatchewan is bordered on the west by Alberta, on the north by the Northwest Territories, on the east by Manitoba, and on the south by the U.S. states of Montana and North Dakota....
, the site of the most recent sample described by Jong Soo Park of Dalhousie University
Dalhousie University
Dalhousie University is a public research university located in Halifax, Nova Scotia, Canada. The university comprises eleven faculties including Schulich School of Law and Dalhousie University Faculty of Medicine. It also includes the faculties of architecture, planning and engineering located at...
in Halifax, NS, Canada.
Russell Vreeland of Ancient Biomaterials Institute of West Chester University in Pennsylvania
Pennsylvania
The Commonwealth of Pennsylvania is a U.S. state that is located in the Northeastern and Mid-Atlantic regions of the United States. The state borders Delaware and Maryland to the south, West Virginia to the southwest, Ohio to the west, New York and Ontario, Canada, to the north, and New Jersey to...
, USA, performed an analysis of all known halopathic bacteria, which yielded the finding that Park's bacteria contained six segments of DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
never seen before in the halopaths. Vreeland also tracked down the buffalo skin and determined that the salt came from the same mine as Park's sample. He has also discovered an even older halopath estimated at 250 million years old in New Mexico
New Mexico
New Mexico is a state located in the southwest and western regions of the United States. New Mexico is also usually considered one of the Mountain States. With a population density of 16 per square mile, New Mexico is the sixth-most sparsely inhabited U.S...
.