Microbial rhodopsin

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Purple bacteriorhodopsin in Halobacteria at Cargill's salt evaporation ponds in San Francisco Bay, located at Newark, California Salt ponds SF Bay (dro!d).jpg
Purple bacteriorhodopsin in Halobacteria at Cargill's salt evaporation ponds in San Francisco Bay, located at Newark, California
Archaeal/bacterial/fungal rhodopsins
1m0l opm.png
Bacteriorhodopsin trimer
Identifiers
SymbolBac_rhodopsin
Pfam PF01036
InterPro IPR001425
SMART SM01021
PROSITE PDOC00291
SCOP2 2brd / SCOPe / SUPFAM
TCDB 3.E.1
OPM superfamily 6
OPM protein 1vgo
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

Microbial rhodopsins, also known as bacterial rhodopsins, are retinal-binding proteins that provide light-dependent ion transport and sensory functions in halophilic [2] [3] and other bacteria. They are integral membrane proteins with seven transmembrane helices, the last of which contains the attachment point (a conserved lysine) for retinal. Most microbial rhodopsins pump inwards, however "mirror rhodopsins" which function outwards. have been discovered. [4]

Contents

This protein family includes light-driven proton pumps, ion pumps and ion channels, as well as light sensors. For example, the proteins from halobacteria include bacteriorhodopsin and archaerhodopsin, which are light-driven proton pumps; halorhodopsin, a light-driven chloride pump; and sensory rhodopsin, which mediates both photoattractant (in the red) and photophobic (in the ultra-violet) responses. Proteins from other bacteria include proteorhodopsin.

As their name indicates, microbial rhodopsins are found in Archaea and Bacteria, and also in Eukaryota (such as algae) and viruses; although they are rare in complex multicellular organisms. [5] [6]

Nomenclature

Rhodopsin was originally a synonym for "visual purple", a visual pigment (light-sensitive molecule) found in the retinas of frogs and other vertebrates, used for dim-light vision, and usually found in rod cells. This is still the meaning of rhodopsin in the narrow sense, any protein evolutionarily homologous to this protein. In a broad non-genetic sense, rhodopsin refers to any molecule, whether related by genetic descent or not (mostly not), consisting of an opsin and a chromophore (generally a variant of retinal). All animal rhodopsins arose (by gene duplication and divergence) late in the history of the large G-protein coupled receptor (GPCR) gene family, which itself arose after the divergence of plants, fungi, choanoflagellates and sponges from the earliest animals. The retinal chromophore is found solely in the opsin branch of this large gene family, meaning its occurrence elsewhere represents convergent evolution, not homology. Microbial rhodopsins are, by sequence, very different from any of the GPCR families. [7]

The term bacterial rhodopsin originally referred to the first microbial rhodopsin discovered, known today as bacteriorhodopsin. The first bacteriorhodopsin turned out to be of archaeal origin, from Halobacterium salinarum . [8] Since then, other microbial rhodopsins have been discovered, rendering the term bacterial rhodopsin ambiguous. [9] [10]

Table

Below is a list of some of the more well-known microbial rhodopsins and some of their properties.

FunctionNameAbbr.Ref.
proton pump (H+) bacteriorhodopsin BR [11]
proton pump (H+) proteorhodopsin PR [11]
proton pump (H+) archaerhodopsin Arch [12]
proton pump (H+)xanthorhodopsinxR [13]
proton pump (H+)Gloeobacter rhodopsinGR [14]
cation channel (+) channelrhodopsin ChR [15]
cation pump (Na+)Krokinobacter eikastus rhodopsin 2KR2 [16]
anion pump (Cl-) halorhodopsin HR [11]
photosensorsensory rhodopsin ISR-I [11]
photosensor sensory rhodopsin II SR-II [11]
photosensor Neurospora opsin INOP-I [15] [17]
light-activated enzymerhodopsin guanylyl cyclaseRhGC [18]

The Ion-Translocating Microbial Rhodopsin Family

The Ion-translocating Microbial Rhodopsin (MR) Family (TC# 3.E.1) is a member of the TOG Superfamily of secondary carriers. Members of the MR family catalyze light-driven ion translocation across microbial cytoplasmic membranes or serve as light receptors. Most proteins of the MR family are all of about the same size (250-350 amino acyl residues) and possess seven transmembrane helical spanners with their N-termini on the outside and their C-termini on the inside. There are 9 subfamilies in the MR family: [19]

  1. Bacteriorhodopsins pump protons out of the cell;
  2. Halorhodopsins pump chloride (and other anions such as bromide, iodide and nitrate) into the cell;
  3. Sensory rhodopsins, which normally function as receptors for phototactic behavior, are capable of pumping protons out of the cell if dissociated from their transducer proteins;
  4. the Fungal Chaperones are stress-induced proteins of ill-defined biochemical function, but this subfamily also includes a H+-pumping rhodopsin; [20]
  5. the bacterial rhodopsin, called Proteorhodopsin, is a light-driven proton pump that functions as does bacteriorhodopsins;
  6. the Neurospora crassa retinal-containing receptor serves as a photoreceptor (Neurospora ospin I); [21]
  7. the green algal light-gated proton channel, Channelrhodopsin-1;
  8. Sensory rhodopsins from cyanobacteria.
  9. Light-activated rhodopsin/guanylyl cyclase

A phylogenetic analysis of microbial rhodopsins and a detailed analysis of potential examples of horizontal gene transfer have been published. [22]

Structure

Among the high resolution structures for members of the MR Family are the archaeal proteins, bacteriorhodopsin, [23] archaerhodopsin, [24] sensory rhodopsin II, [25] halorhodopsin, [26] as well as an Anabaena cyanobacterial sensory rhodopsin (TC# 3.E.1.1.6) [27] and others.

Function

The association of sensory rhodopsins with their transducer proteins appears to determine whether they function as transporters or receptors. Association of a sensory rhodopsin receptor with its transducer occurs via the transmembrane helical domains of the two interacting proteins. There are two sensory rhodopsins in any one halophilic archaeon, one (SRI) that responds positively to orange light but negatively to blue light, the other (SRII) that responds only negatively to blue light. Each transducer is specific for its cognate receptor. An x-ray structure of SRII complexed with its transducer (HtrII) at 1.94 Å resolution is available ( 1H2S ​). [28] Molecular and evolutionary aspects of the light-signal transduction by microbial sensory receptors have been reviewed. [29]

Homologues

Homologues include putative fungal chaperone proteins, a retinal-containing rhodopsin from Neurospora crassa , [30] a H+-pumping rhodopsin from Leptosphaeria maculans, [20] retinal-containing proton pumps isolated from marine bacteria, [31] a green light-activated photoreceptor in cyanobacteria that does not pump ions and interacts with a small (14 kDa) soluble transducer protein [27] [32] and light-gated H+ channels from the green alga, Chlamydomonas reinhardtii . [33] The N. crassa NOP-1 protein exhibits a photocycle and conserved H+ translocation residues that suggest that this putative photoreceptor is a slow H+ pump. [20] [34] [35]

Most of the MR family homologues in yeast and fungi are of about the same size and topology as the archaeal proteins (283-344 amino acyl residues; 7 putative transmembrane α-helical segments), but they are heat shock- and toxic solvent-induced proteins of unknown biochemical function. They have been suggested to function as pmf-driven chaperones that fold extracellular proteins, but only indirect evidence supports this postulate. [21] The MR family is distantly related to the 7 TMS LCT family (TC# 2.A.43). [21] Representative members of MR family can be found in the Transporter Classification Database.

Bacteriorhodopsin

Bacteriorhodopsin pumps one H+ ion, from the cytosol to the extracellular medium, per photon absorbed. Specific transport mechanisms and pathways have been proposed. [26] [36] [37] The mechanism involves:

  1. photo-isomerization of the retinal and its initial configurational changes,
  2. deprotonation of the retinal Schiff base and the coupled release of a proton to the extracellular membrane surface,
  3. the switch event that allows reprotonation of the Schiff base from the cytoplasmic side.

Six structural models describe the transformations of the retinal and its interaction with water 402, Asp85, and Asp212 in atomic detail, as well as the displacements of functional residues farther from the Schiff base. The changes provide rationales for how relaxation of the distorted retinal causes movements of water and protein atoms that result in vectorial proton transfers to and from the Schiff base. [36] Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin. [38]

Most residues participating in the trimerization are not conserved in bacteriorhodopsin, a homologous protein capable of forming a trimeric structure in the absence of bacterioruberin. Despite a large alteration in the amino acid sequence, the shape of the intratrimer hydrophobic space filled by lipids is highly conserved between archaerhodopsin-2 and bacteriorhodopsin. Since a transmembrane helix facing this space undergoes a large conformational change during the proton pumping cycle, it is feasible that trimerization is an important strategy to capture special lipid components that are relevant to the protein activity. [39]

Archaerhodopsin

Ground state structure of Archaerhodopsin-3, showing the covalently bound retinal group: PDB:6S6C. Archaerhodopsin-3 6S6C.gif
Ground state structure of Archaerhodopsin-3, showing the covalently bound retinal group: PDB:6S6C.

Archaerhodopsins are light-driven H+ ion transporters. They differ from bacteriorhodopsin in that the claret membrane, in which they are expressed, includes bacterioruberin, a second chromophore thought to protect against photobleaching. Bacteriorhodopsin also lacks the omega loop structure that has been observed at the N-terminus of the structures of several archaerhodopsins.

Archaerhodopsin-2 (AR2) is found in the claret membrane of Halorubrum sp. It is a light-driven proton pump. Trigonal and hexagonal crystals revealed that trimers are arranged on a honeycomb lattice. [39] In these crystals, bacterioruberin binds to crevices between the subunits of the trimer. The polyene chain of the second chromophore is inclined from the membrane normal by an angle of about 20 degrees and, on the cytoplasmic side, it is surrounded by helices AB and DE of neighboring subunits. This peculiar binding mode suggests that bacterioruberin plays a structural role for the trimerization of AR2. When compared with the aR2 structure in another crystal form containing no bacterioruberin, the proton release channel takes a more closed conformation in the P321 or P6(3) crystal; i.e., the native conformation of protein is stabilized in the trimeric protein-bacterioruberin complex.

Mutants of Archaerhodopsin-3 (AR3) are widely used as tools in optogenetics for neuroscience research. [40]

Channelrhodopsins

Channelrhodopsin-1 (ChR1) or channelopsin-1 (Chop1; Cop3; CSOA) of C. reinhardtii is closely related to the archaeal sensory rhodopsins. It has 712 aas with a signal peptide, followed by a short amphipathic region, and then a hydrophobic N-terminal domain with seven probable TMSs (residues 76-309) followed by a long hydrophilic C-terminal domain of about 400 residues. Part of the C-terminal hydrophilic domain is homologous to intersection (EH and SH3 domain protein 1A) of animals (AAD30271).

Chop1 serves as a light-gated proton channel and mediates phototaxis and photophobic responses in green algae. [33] Based on this phenotype, Chop1 could be assigned to TC category #1.A, but because it belongs to a family in which well-characterized homologues catalyze active ion transport, it is assigned to the MR family. Expression of the chop1 gene, or a truncated form of that gene encoding only the hydrophobic core (residues 1-346 or 1–517) in frog oocytes in the presence of all-trans retinal produces a light-gated conductance that shows characteristics of a channel passively but selectively permeable to protons. This channel activity probably generates bioelectric currents. [33]

A homologue of ChR1 in C. reinhardtii is channelrhodopsin-2 (ChR2; Chop2; Cop4; CSOB). This protein is 57% identical, 10% similar to ChR1. It forms a cation-selective ion channel activated by light absorption. It transports both monovalent and divalent cations. It desensitizes to a small conductance in continuous light. Recovery from desensitization is accelerated by extracellular H+ and a negative membrane potential. It may be a photoreceptor for dark adapted cells. [41] A transient increase in hydration of transmembrane α-helices with a t(1/2) = 60 μs tallies with the onset of cation permeation. Aspartate 253 accepts the proton released by the Schiff base (t(1/2) = 10 μs), with the latter being reprotonated by aspartic acid 156 (t(1/2) = 2 ms). The internal proton acceptor and donor groups, corresponding to D212 and D115 in bacteriorhodopsin, are clearly different from other microbial rhodopsins, indicating that their spatial positions in the protein were relocated during evolution. E90 deprotonates exclusively in the nonconductive state. The observed proton transfer reactions and the protein conformational changes relate to the gating of the cation channel. [42]

Halorhodopsins

Bacteriorhodopsin pumps one Cl− ion, from the extracellular medium into the cytosol, per photon absorbed. Although the ions move in the opposite direction, the current generated (as defined by the movement of positive charge) is the same as for bacteriorhodopsin and the archaerhodopsins.

Marine Bacterial Rhodopsin

A marine bacterial rhodopsin has been reported to function as a proton pump. However, it also resembles sensory rhodopsin II of archaea as well as an Orf from the fungus Leptosphaeria maculans (AF290180). These proteins exhibit 20-30% identity with each other.

Transport Reaction

The generalized transport reaction for bacterio- and sensory rhodopsins is: [19]

H+ (in) + hν → H+ (out).

That for halorhodopsin is:

Cl− (out) + hν → Cl− (in).

See also

Related Research Articles

<span class="mw-page-title-main">Transmembrane protein</span> Protein spanning across a biological membrane

A transmembrane protein is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently undergo significant conformational changes to move a substance through the membrane. They are usually highly hydrophobic and aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of them (beta-barrels) can be also extracted using denaturing agents.

<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">Proteorhodopsin</span> Family of transmembrane proteins

Proteorhodopsin 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.

<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.

Channelrhodopsins are a subfamily of retinylidene proteins (rhodopsins) that function as light-gated ion channels. They serve as sensory photoreceptors in unicellular green algae, controlling phototaxis: movement in response to light. Expressed in cells of other organisms, they enable light to control electrical excitability, intracellular acidity, calcium influx, and other cellular processes. Channelrhodopsin-1 (ChR1) and Channelrhodopsin-2 (ChR2) from the model organism Chlamydomonas reinhardtii are the first discovered channelrhodopsins. Variants that are sensitive to different colors of light or selective for specific ions have been cloned from other species of algae and protists.

<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.

<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.

Light-gated ion channels are a family of ion channels regulated by electromagnetic radiation. Other gating mechanisms for ion channels include voltage-gated ion channels, ligand-gated ion channels, mechanosensitive ion channels, and temperature-gated ion channels. Most light-gated ion channels have been synthesized in the laboratory for study, although two naturally occurring examples, channelrhodopsin and anion-conducting channelrhodopsin, are currently known. Photoreceptor proteins, which act in a similar manner to light-gated ion channels, are generally classified instead as G protein-coupled receptors.

Optogenetics is a biological technique to control the activity of neurons or other cell types with light. This is achieved by expression of light-sensitive ion channels, pumps or enzymes specifically in the target cells. On the level of individual cells, light-activated enzymes and transcription factors allow precise control of biochemical signaling pathways. In systems neuroscience, the ability to control the activity of a genetically defined set of neurons has been used to understand their contribution to decision making, learning, fear memory, mating, addiction, feeding, and locomotion. In a first medical application of optogenetic technology, vision was partially restored in a blind patient with Retinitis pigmentosa.

<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">Peter Hegemann</span> German biophysicist

Peter Hegemann is a Hertie Senior Research Chair for Neurosciences and a professor of Experimental Biophysics at the Department of Biology, Faculty of Life Sciences, Humboldt University of Berlin, Germany. He is known for his discovery of channelrhodopsin, a type of ion channels regulated by light, thereby serving as a light sensor. This created the field of optogenetics, a technique that controls the activities of specific neurons by applying light. He has received numerous accolades, including the Rumford Prize, the Shaw Prize in Life Science and Medicine, and the Albert Lasker Award for Basic Medical Research.

<span class="mw-page-title-main">Anion-conducting channelrhodopsin</span> Class of light-gated ion channels

Anion-conducting channelrhodopsins are light-gated ion channels that open in response to light and let negatively charged ions enter a cell. All channelrhodopsins use retinal as light-sensitive pigment, but they differ in their ion selectivity. Anion-conducting channelrhodopsins are used as tools to manipulate brain activity in mice, fruit flies and other model organisms (Optogenetics). Neurons expressing anion-conducting channelrhodopsins are silenced when illuminated with light, an effect that has been used to investigate information processing in the brain. For example, suppressing dendritic calcium spikes in specific neurons with light reduced the ability of mice to perceive a light touch to a whisker. Studying how the behavior of an animal changes when specific neurons are silenced allows scientists to determine the role of these neurons in the complex circuits controlling behavior.

<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.

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

Georg Nagel is a biophysicist and professor at the Department for Neurophysiology at the University of Würzburg in Germany. His research is focused on microbial photoreceptors and the development of optogenetic tools.

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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