Proteorhodopsin

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Proteorhodopsin
PR surface visualization - ELViture April 2016.png
Proteorhodopsin Cartoon Visualization by ELViture
Identifiers
SymbolBac_rhodopsin
InterPro IPR017402
SCOP2 2brd / SCOPe / SUPFAM
TCDB 3.E.1
OPM superfamily 6
OPM protein 4hyj

Proteorhodopsin (also known as pRhodopsin) is a family of transmembrane proteins that use retinal as a chromophore for light-mediated functionality, in this case, a proton pump. pRhodopsin is found in marine planktonic bacteria, archaea and eukaryotes (protae), but was first discovered in bacteria. [1] [2] [3] [4]

Contents

Its name is derived from proteobacteria (now called Pseudomonadota) that were named after Ancient Greek Πρωτεύς (Proteus), an early sea god mentioned by Homer as "Old Man of the Sea", Ῥόδος (rhódon) for "rose", due to its pinkish color, and ὄψις (opsis) for "sight". Some members of the family, Homologous rhodopsin-like pigments, i.e. bacteriorhodopsin (of which there are more than 800 types) have Sensory Functions like opsins, integral for visual phototransduction. Many of these sensory functions are unknown – for example, the function of Neuropsin in the human retina. [5] Members are known to have different absorption spectra including green and blue visible light. [6] [7] [8] [9] [10] [11]

History

Proteorhodopsin (PR or pRhodopsin) was first discovered in 2000 within a bacterial artificial chromosome from previously uncultivated marine Gammaproteobacteria, still only referred to by their ribotype metagenomic data, SAR86. More species of Gammaproteobacteria, both Gram-positive and Gram-negative, were found to express the protein. [1]

Distribution

Samples of proteorhodopsin expressing bacteria have been obtained from the Eastern Pacific Ocean, Central North Pacific Ocean and Southern Ocean, Antarctica. [12] Subsequently, genes of proteorhodopsin variants have been identified in samples from the Mediterranean, Red Seas, the Sargasso Sea, and Sea of Japan, and the North Sea. [4] [6]

Proteorhodopsin variants are not spread randomly, but disperse along depth gradients based on the maximal absorption-tuning of the particular holoprotein sequence; this is mainly due to the electromagnetic absorption by water which creates wavelength gradients relative to depth. Oxyrrhis marina is a dinoflagellate protist with green-absorbing proteorhodopsin (a result of the L109 Group) that exists mostly in shallow tide pools and shores, where green light is still available. Karlodinium micrum , another dinolagelate, expresses a blue tuned proteorhodopsin (E109) which may be related to its deep water vertical migrations. [3] O. marina was originally believed to be a heterotroph, however the proteorhodopsin may well partake in a functionally significant manner, as it was the most abundantly expressed nuclear gene and, furthermore, is dispersed unevenly in the organism, suggesting some organelle membrane function. Previously the only known eukaryotic solar energy transducing proteins were Photosystem I and Photosystem II. It has been hypothesized that lateral gene transfer is the method by which proteorhodopsin has made its way into numerous phyla. Bacteria, archaea and eukarya all colonize the photic zone where they come to light; Proteorhodopsin has been able to disseminate through this zone, but not to other portions of the water column. [3] [4] [9] [13] [14]

Taxonomy

Proteorhodopsin belongs to a family of similar retinylidene proteins, most similar to its archaeal homologues halorhodopsin and bacteriorhodopsin. Sensory rhodopsin was discovered by Franz Christian Boll in 1876. [11] [15] Bacteriorhodopsin was discovered in 1971 and named in 1973 and is currently only known to exist in archaea, not bacteria. [16] Halorhodopsin was first discovered and named in 1977. [17] Bacteriorhodopsin and Halorhodopsin both only exist in archaea whereas proteorhodopsin spans bacteria, archaea, and eukaryotes. Proteorhodopsin shares seven transmembrane α-helices retinal covalently linked by a Schiff base mechanism to a lysine residue in the seventh helix (helix G). Bacteriorhodopsin, like proteorhodopsin, is a light-driven proton pump. Sensory rhodopsin is a G-coupled protein involved in sight. [1] [17]

Active site

2L6x In-Active-Site Cartoon Color Coded and Labeled Visualization, D and E Helices hidden for vantage, Retinal ligand binding site In-Active-Site Visualization, D and E Helicies hidden for vantag. ELViture 4-16 .png
2L6x In-Active-Site Cartoon Color Coded and Labeled Visualization, D and E Helices hidden for vantage, Retinal ligand binding site

In comparison with its better-known archaeal homolog bacteriorhodopsin, most of the active site residues of known importance to the bacteriorhodopsin mechanism are conserved in proteorhodopsin. Sequence similarity is not significantly conserved however, from either halo- or bacterio- rhodopsin. Homologues of the active site residues Arg82, Asp85 (the primary proton acceptor), Asp212 and Lys216 (the retinal 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 (or Glu 108 and 204 depending on the bacRhodopsin variant), which are thought to be involved in the proton release pathway at the extracellular surface. However, Asp97 and Arg94 may replace this functionality without the close residue proximity as in bacteriorhodopsin. The department of chemistry at Syracuse University decisively showed Asp97 cannot be the proton release group as the release happened at forcing conditions under which the aspartic acid group remained protonated. [18] [19] [20] [21]

Ligand

Visualization of the retinal bound active site of the 2L6X protein structure of pRhodopsin, residues color coded and labeled by activity, ligand is orange. 2L6X Active Site Visualization E.Vitureira.png
Visualization of the retinal bound active site of the 2L6X protein structure of pRhodopsin, residues color coded and labeled by activity, ligand is orange.

The Rhodopsin haloprotein family shares the ligand retinal, one of the many types of Vitamin A. Retinal is a conjugated poly-unsaturated chromophore (polyene), obtained from carnivorous diet or by the carotene pathway (β-carotene 15,15'-monoxygenase).

Function

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 proteorhodopsin 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 [18] , and isomerizes 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. [18] [20] [21] [22] Complete proteorhodopsin based photosystems have been discovered and expressed in E. coli, giving them additional light mediated energy gradient capability for ATP generation without external need for retinal or precursors; with the PR, gene five other proteins code for the photopigment biosynthetic pathway. [23]

Genetic engineering

If the gene for proteorhodopsin is inserted into E. coli and retinal is given to these modified bacteria, then they will incorporate the pigment into their cell membrane and will pump H+ in the presence of light. A deep purple is representative of clearly transformed colonies, due to light absorption. Proton gradients can be used to power other membrane protein structures or used to acidify a vesicle type organelle. [1] It was further demonstrated that the proton gradient generated by proteorhodopsin could be used to generate ATP. [23]

See also

Related Research Articles

<span class="mw-page-title-main">Rhodopsin</span> Light-sensitive receptor protein

Rhodopsin, also known as visual purple, is a protein encoded by the RHO gene and a G-protein-coupled receptor (GPCR). It is the opsin of the rod cells in the retina and a light-sensitive receptor protein that triggers visual phototransduction in rods. Rhodopsin mediates dim light vision and thus is extremely sensitive to light. When rhodopsin is exposed to light, it immediately photobleaches. In humans, it is regenerated fully in about 30 minutes, after which the rods are more sensitive. Defects in the rhodopsin gene cause eye diseases such as retinitis pigmentosa and congenital stationary night blindness.

<span class="mw-page-title-main">Bacteriorhodopsin</span> Protein used by single-celled organisms

Bacteriorhodopsin (Bop) is a protein used by Archaea, most notably by haloarchaea, a class of the Euryarchaeota. 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. The resulting proton gradient is subsequently converted into chemical energy.

<span class="mw-page-title-main">Retinal</span> Chemical compound

Retinal is a polyene chromophore. Retinal, bound to proteins called opsins, is the chemical basis of visual phototransduction, the light-detection stage of visual perception (vision).

<span class="mw-page-title-main">Opsin</span> Class of light-sensitive proteins

Animal opsins are G-protein-coupled receptors and a group of proteins made light-sensitive via a chromophore, typically retinal. When bound to retinal, opsins become retinylidene proteins, but are usually still called opsins regardless. Most prominently, they are found in photoreceptor cells of the retina. Five classical groups of opsins are involved in vision, mediating the conversion of a photon of light into an electrochemical signal, the first step in the visual transduction cascade. Another opsin found in the mammalian retina, melanopsin, is involved in circadian rhythms and pupillary reflex but not in vision. Humans have in total nine opsins. Beside vision and light perception, opsins may also sense temperature, sound, or chemicals.

Photoheterotrophs are heterotrophic phototrophs—that is, they are organisms that use light for energy, but cannot use carbon dioxide as their sole carbon source. Consequently, they use organic compounds from the environment to satisfy their carbon requirements; these compounds include carbohydrates, fatty acids, and alcohols. Examples of photoheterotrophic organisms include purple non-sulfur bacteria, green non-sulfur bacteria, and heliobacteria. These microorganisms are ubiquitous in aquatic habitats, occupy unique niche-spaces, and contribute to global biogeochemical cycling. Recent research has also indicated that the oriental hornet and some aphids may be able to use light to supplement their energy supply.

<i>Halobacterium</i> Genus of archaea

Halobacterium is a genus in the family Halobacteriaceae.

<span class="mw-page-title-main">Halorhodopsin</span> Family of transmembrane proteins


Halorhodopsin is a seven-transmembrane retinylidene protein from microbial rhodopsin family. It is a chloride-specific light-activated ion pump found in archaea known as halobacteria. It is activated by green light wavelengths of approximately 578nm. Halorhodopsin also shares sequence similarity to channelrhodopsin, a light-gated ion channel.

Photoreceptor proteins are light-sensitive proteins involved in the sensing and response to light in a variety of organisms. Some examples are rhodopsin in the photoreceptor cells of the vertebrate retina, phytochrome in plants, and bacteriorhodopsin and bacteriophytochromes in some bacteria. They mediate light responses as varied as visual perception, phototropism and phototaxis, as well as responses to light-dark cycles such as circadian rhythm and other photoperiodisms including control of flowering times in plants and mating seasons in animals.

Retinylidene proteins, or rhodopsins in a broad sense, are proteins that use retinal as a chromophore for light reception. They are the molecular basis for a variety of light-sensing systems from phototaxis in flagellates to eyesight in animals. Retinylidene proteins include all forms of opsin and rhodopsin. While rhodopsin in the narrow sense refers to a dim-light visual pigment found in vertebrates, usually on rod cells, rhodopsin in the broad sense refers to any molecule consisting of an opsin and a retinal chromophore in the ground state. When activated by light, the chromophore is isomerized, at which point the molecule as a whole is no longer rhodopsin, but a related molecule such as metarhodopsin. However, it remains a retinylidene protein. The chromophore then separates from the opsin, at which point the bare opsin is a retinylidene protein. Thus, the molecule remains a retinylidene protein throughout the phototransduction cycle.

<i>Halobacterium salinarum</i> Species of archaeon

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.

<span class="mw-page-title-main">Retinalophototroph</span>

A retinalophototroph is one of two different types of phototrophs, and are named for retinal-binding proteins they utilize for cell signaling and converting light into energy. Like all phototrophs, retinalophototrophs absorb photons to initiate their cellular processes. In contrast with chlorophototrophs, retinalophototrophs do not use chlorophyll or an electron transport chain to power their chemical reactions. This means retinalophototrophs are incapable of traditional carbon fixation, a fundamental photosynthetic process that transforms inorganic carbon into organic compounds. For this reason, experts consider them to be less efficient than their chlorophyll-using counterparts, chlorophototrophs.

<span class="mw-page-title-main">Photosynthetic reaction centre protein family</span>

Photosynthetic reaction centre proteins are main protein components of photosynthetic reaction centres (RCs) of bacteria and plants. They are transmembrane proteins embedded in the chloroplast thylakoid or bacterial cell membrane.

<span class="mw-page-title-main">Bacterial motility</span> Ability of bacteria to move independently using metabolic energy

Bacterial motility is the ability of bacteria to move independently using metabolic energy. Most motility mechanisms that evolved among bacteria also evolved in parallel among the archaea. Most rod-shaped bacteria can move using their own power, which allows colonization of new environments and discovery of new resources for survival. Bacterial movement depends not only on the characteristics of the medium, but also on the use of different appendages to propel. Swarming and swimming movements are both powered by rotating flagella. Whereas swarming is a multicellular 2D movement over a surface and requires the presence of surfactants, swimming is movement of individual cells in liquid environments.

<span class="mw-page-title-main">Phototaxis</span>

Phototaxis is a kind of taxis, or locomotory movement, that occurs when a whole organism moves towards or away from a stimulus of light. This is advantageous for phototrophic organisms as they can orient themselves most efficiently to receive light for photosynthesis. Phototaxis is called positive if the movement is in the direction of increasing light intensity and negative if the direction is opposite.

<span class="mw-page-title-main">Sensory rhodopsin II</span>

Sensory rhodopsin II (SRII), also known as pharaonis phoborhodopsin (ppR), is a membrane protein of archaea, responsible generating the phototaxis signal. Sensory rhodopsin II is found in Halobacterium salinarum and Natronomonas pharaonis.

<span class="mw-page-title-main">Microbial rhodopsin</span> Retinal-binding proteins

Microbial rhodopsins, also known as bacterial rhodopsins, are retinal-binding proteins that provide light-dependent ion transport and sensory functions in halophilic and other bacteria. They are integral membrane proteins with seven transmembrane helices, the last of which contains the attachment point for retinal. Most microbial rhodopsins pump inwards, however "mirror rhodopsins" which function outwards. have been discovered.

<span class="mw-page-title-main">Oded Beja</span>

Oded Béjà is a professor in the Technion-Israel Institute of Technology, in the field of marine microbiology and metagenomics.

<span class="mw-page-title-main">Archaerhodopsin</span> Family of archaea

Archaerhodopsin proteins are a family of retinal-containing photoreceptors found in the archaea genera Halobacterium and Halorubrum. Like the homologous bacteriorhodopsin (bR) protein, archaerhodopsins harvest energy from sunlight to pump H+ ions out of the cell, establishing a proton motive force that is used for ATP synthesis. They have some structural similarities to the mammalian G protein-coupled receptor protein rhodopsin, but are not true homologs.

Dokdonia is a genus of bacteria in the family Flavobacteriaceae and phylum Bacteroidota.

Dieter Oesterhelt was a German biochemist. From 1980 until 2008, he was director of the Max Planck Institute for Biochemistry, Martinsried.

References

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