Proteorhodopsin
Encyclopedia
Proteorhodopsin is a photoactive retinylidene protein
in marine bacterioplanktons and eukaryotes. Just like the homologous
pigment bacteriorhodopsin
found in some archaea
, it consists of a transmembrane protein
bound to a retinal
molecule and functions as a light-driven proton pump
. Some members of the family (of more than 800 types) are believed to have sensory functions. Members are known to have different absorption spectra.
Proteorhodopsin was first discovered in 2000. It was found in the genomes of several species of uncultivated marine γ-proteobacteria
present in the Eastern Pacific Ocean
, Central North Pacific Ocean and Southern Ocean
, Antarctica. Subsequently, genes of proteorhodopsin variants have been identified in samples from the Mediterranean and Red Sea
s and the Sargasso Sea
and the Sea of Japan
. These variants are not spread randomly, but have different distributions of absorption maxima along depth gradients and across locations.
On comparison to its better-known archaeal homolog bacteriorhodopsin, most of the active site residues of known importance to the bacteriorhodopsin mechanism are conserved in proteorhodopsin. Homologues of the active site
residue
s Arg
82, Asp85 (the primary proton
acceptor), Asp212 and Lys
216 (the retina
l Schiff base
binding site) in bacteriorhodopsin are conserved as Arg94, Asp97, Asp227 and Lys231 in proteorhodopsin. However, in proteorhodopsin, there are no carboxylic acid
residues directly homologous to Glu194 or Glu204 of bacteriorhodopsin, which are thought to be involved in the proton release pathway at the extracellular surface.
It seems likely that proteorhodopsin functions throughout the Earth's oceans as a light-driven H+ pump, by a mechanism similar to that of bacteriorhodopsin. As in bacteriorhodopsin, the retinal chromophore
of bacteriorhodopsin is covalently bound to the apoprotein
via a protonated Schiff base
at Lys231. The configuration of the retinal chromophore in unphotolyzed proteorhodopsin is predominantly all-trans, and changes to 13-cis upon illumination with light. Several models of the complete proteorhodopsin photocycle have been proposed, based on FTIR and UV–visible spectroscopy
; they resemble established photocycle models for bacteriorhodopsin.
and retinal is given to these modified bacteria
, then they will incorporate the pigment
into their cell membrane
and will pump protons in the presence of light. It was further demonstrated that the proton gradient generated by proteorhodopsin could be used to generate ATP.
Retinylidene protein
Retinylidene proteins are a family of proteins that use retinal as chromophore for light reception. Proteins of this family are also called opsins...
in marine bacterioplanktons and eukaryotes. Just like the homologous
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
pigment 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...
found in some archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
, it consists of a transmembrane protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
bound to a 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...
molecule and functions as a light-driven proton pump
Proton pump
A proton pump is an integral membrane protein that is capable of moving protons across a cell membrane, mitochondrion, or other organelle. Mechanisms are based on conformational changes of the protein structure or on the Q cycle.-Function:...
. Some members of the family (of more than 800 types) are believed to have sensory functions. Members are known to have different absorption spectra.
Proteorhodopsin was first discovered in 2000. It was found in the genomes of several species of uncultivated marine γ-proteobacteria
Proteobacteria
The Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera....
present in the Eastern Pacific Ocean
Pacific Ocean
The Pacific Ocean is the largest of the Earth's oceanic divisions. It extends from the Arctic in the north to the Southern Ocean in the south, bounded by Asia and Australia in the west, and the Americas in the east.At 165.2 million square kilometres in area, this largest division of the World...
, Central North Pacific Ocean and Southern Ocean
Southern Ocean
The Southern Ocean comprises the southernmost waters of the World Ocean, generally taken to be south of 60°S latitude and encircling Antarctica. It is usually regarded as the fourth-largest of the five principal oceanic divisions...
, Antarctica. Subsequently, genes of proteorhodopsin variants have been identified in samples from the Mediterranean and Red Sea
Red Sea
The Red Sea is a seawater inlet of the Indian Ocean, lying between Africa and Asia. The connection to the ocean is in the south through the Bab el Mandeb strait and the Gulf of Aden. In the north, there is the Sinai Peninsula, the Gulf of Aqaba, and the Gulf of Suez...
s and the Sargasso Sea
Sargasso Sea
The Sargasso Sea is a region in the middle of the North Atlantic Ocean, surrounded by ocean currents. It is bounded on the west by the Gulf Stream; on the north, by the North Atlantic Current; on the east, by the Canary Current; and on the south, by the North Atlantic Equatorial Current. This...
and the Sea of Japan
Sea of Japan
The Sea of Japan is a marginal sea of the western Pacific Ocean, between the Asian mainland, the Japanese archipelago and Sakhalin. It is bordered by Japan, North Korea, Russia and South Korea. Like the Mediterranean Sea, it has almost no tides due to its nearly complete enclosure from the Pacific...
. These variants are not spread randomly, but have different distributions of absorption maxima along depth gradients and across locations.
On comparison to its better-known archaeal homolog bacteriorhodopsin, most of the active site residues of known importance to the bacteriorhodopsin mechanism are conserved in proteorhodopsin. Homologues of the active site
Active site
In biology the active site is part of an enzyme where substrates bind and undergo a chemical reaction. The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues that...
residue
Residue (chemistry)
In chemistry, residue is the material remaining after a distillation or an evaporation, or to a portion of a larger molecule, such as a methyl group. It may also refer to the undesired byproducts of a reaction....
s Arg
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...
82, Asp85 (the primary proton
Proton
The proton is a subatomic particle with the symbol or and a positive electric charge of 1 elementary charge. One or more protons are present in the nucleus of each atom, along with neutrons. The number of protons in each atom is its atomic number....
acceptor), Asp212 and Lys
Lysine
Lysine is an α-amino acid with the chemical formula HO2CCH4NH2. It is an essential amino acid, which means that the human body cannot synthesize it. Its codons are AAA and AAG....
216 (the retina
Retina
The vertebrate retina is a light-sensitive tissue lining the inner surface of the eye. The optics of the eye create an image of the visual world on the retina, which serves much the same function as the film in a camera. Light striking the retina initiates a cascade of chemical and electrical...
l Schiff base
Schiff base
A Schiff base, named after Hugo Schiff, is a compound with a functional group that contains a carbon-nitrogen double bond with the nitrogen atom connected to an aryl or alkyl group, not hydrogen....
binding site) in bacteriorhodopsin are conserved as Arg94, Asp97, Asp227 and Lys231 in proteorhodopsin. However, in proteorhodopsin, there are no carboxylic acid
Carboxylic acid
Carboxylic acids are organic acids characterized by the presence of at least one carboxyl group. The general formula of a carboxylic acid is R-COOH, where R is some monovalent functional group...
residues directly homologous to Glu194 or Glu204 of bacteriorhodopsin, which are thought to be involved in the proton release pathway at the extracellular surface.
It seems likely that proteorhodopsin functions throughout the Earth's oceans as a light-driven H+ pump, by a mechanism similar to that of bacteriorhodopsin. As in bacteriorhodopsin, the retinal chromophore
Chromophore
A chromophore is the part of a molecule responsible for its color. The color arises when a molecule absorbs certain wavelengths of visible light and transmits or reflects others. The chromophore is a region in the molecule where the energy difference between two different molecular orbitals falls...
of bacteriorhodopsin is covalently bound to the apoprotein
Apoprotein
Apoprotein can refer to:*Apoenzyme, the protein part of an enzyme without its characteristic prosthetic group.*Apolipoprotein, a lipid-binding protein that is a constituent of the plasma lipoprotein....
via a protonated Schiff base
Schiff base
A Schiff base, named after Hugo Schiff, is a compound with a functional group that contains a carbon-nitrogen double bond with the nitrogen atom connected to an aryl or alkyl group, not hydrogen....
at Lys231. The configuration of the retinal chromophore in unphotolyzed proteorhodopsin is predominantly all-trans, and changes to 13-cis upon illumination with light. Several models of the complete proteorhodopsin photocycle have been proposed, based on FTIR and UV–visible spectroscopy
Spectroscopy
Spectroscopy is the study of the interaction between matter and radiated energy. Historically, spectroscopy originated through the study of visible light dispersed according to its wavelength, e.g., by a prism. Later the concept was expanded greatly to comprise any interaction with radiative...
; they resemble established photocycle models for bacteriorhodopsin.
Genetic engineering with proteorhodopsins
If the gene for proteorhodopsin is inserted into 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 retinal is given to these modified bacteria
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...
, then they will incorporate the pigment
Pigment
A pigment is a material that changes the color of reflected or transmitted light as the result of wavelength-selective absorption. This physical process differs from fluorescence, phosphorescence, and other forms of luminescence, in which a material emits light.Many materials selectively absorb...
into their cell membrane
Cell membrane
The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. It basically protects the cell...
and will pump protons in the presence of light. It was further demonstrated that the proton gradient generated by proteorhodopsin could be used to generate ATP.