Microbial rhodopsin

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.{{cite journal | vauthors = Nordström KJ, Sällman Almén M, Edstam MM, Fredriksson R, Schiöth HB | title = Independent HHsearch, Needleman--Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families | journal = Molecular Biology and Evolution | volume = 28 | issue = 9 | pages = 2471–80 | date = September 2011 | pmid = 21402729 | doi = 10.1093/molbev/msr061 | doi-access = }}

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.{{cite journal | vauthors = Grote M, O'Malley MA | title = Enlightening the life sciences: the history of halobacterial and microbial rhodopsin research | journal = FEMS Microbiology Reviews | volume = 35 | issue = 6 | pages = 1082–99 | date = November 2011 | pmid = 21623844 | doi = 10.1111/j.1574-6976.2011.00281.x | doi-access = free }} Since then, other microbial rhodopsins have been discovered, rendering the term bacterial rhodopsin ambiguous.{{cite encyclopedia |date=19 December 2012 |title =rhodopsin, n. |encyclopedia=OED Online |publisher=Oxford University Press |url=http://www.oed.com/view/Entry/165304 }}{{cite book| vauthors = Mason P |title=Medical Neurobiology|url=https://books.google.com/books?id=IcRqgPnstUUC&pg=PA375|access-date=21 September 2015|date=26 May 2011|publisher=OUP USA|isbn=978-0-19-533997-0|page=375}}

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

The ion-translocating microbial rhodopsin (MR) family ({{cite web |title = TC# 3.E.1 |website = Transporter Classification Database (tcdb.org) |url = http://www.tcdb.org/search/result.php?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 nine subfamilies in the MR family:{{cite web |last = Saier |first = M.H., Jr. |title = 3.E.1 The ion-translocating microbial rhodopsin (MR) family |website = Transporter Classification Database (tcdb.org) |publisher = Saier Lab Bioinformatics Group (SDSC) |url = http://www.tcdb.org/search/result.php?tc=3.E.1#ref9955}}

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;{{cite journal | vauthors = Waschuk SA, Bezerra AG, Shi L, Brown LS | title = Leptosphaeria rhodopsin: bacteriorhodopsin-like proton pump from a eukaryote | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 19 | pages = 6879–83 | date = May 2005 | pmid = 15860584 | pmc = 1100770 | doi = 10.1073/pnas.0409659102 | bibcode = 2005PNAS..102.6879W | doi-access = free }}
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);{{cite journal | vauthors = Zhai Y, Heijne WH, Smith DW, Saier MH | title = Homologues of archaeal rhodopsins in plants, animals and fungi: structural and functional predications for a putative fungal chaperone protein | journal = Biochimica et Biophysica Acta (BBA) - Biomembranes | volume = 1511 | issue = 2 | pages = 206–23 | date = April 2001 | pmid = 11286964 | doi = 10.1016/s0005-2736(00)00389-8 | s2cid = 7931370 | doi-access = }}
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.{{cite journal | vauthors = Sharma AK, Spudich JL, Doolittle WF | title = Microbial rhodopsins: functional versatility and genetic mobility | journal = Trends in Microbiology | volume = 14 | issue = 11 | pages = 463–9 | date = November 2006 | pmid = 17008099 | doi = 10.1016/j.tim.2006.09.006 }}

Among the high resolution structures for members of the MR Family are the archaeal proteins, bacteriorhodopsin,{{cite journal | vauthors = Luecke H, Schobert B, Richter HT, Cartailler JP, Lanyi JK | title = Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution | journal = Science | volume = 286 | issue = 5438 | pages = 255–61 | date = October 1999 | pmid = 10514362 | doi = 10.1126/science.286.5438.255 }} archaerhodopsin,{{cite journal | vauthors = Bada Juarez JF, Judge PJ, Adam S, Axford D, Vinals J, Birch J, Kwan TO, Hoi KK, Yen HY, Vial A, Milhiet PE, Robinson CV, Schapiro I, Moraes I, Watts A | display-authors = 6 | title = Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization | journal = Nature Communications | volume = 12 | issue = 1 | pages = 629 | date = January 2021 | pmid = 33504778 | pmc = 7840839 | doi = 10.1038/s41467-020-20596-0 | bibcode = 2021NatCo..12..629B }} sensory rhodopsin II,{{cite journal | vauthors = Royant A, Nollert P, Edman K, Neutze R, Landau EM, Pebay-Peyroula E, Navarro J | title = X-ray structure of sensory rhodopsin II at 2.1-A resolution | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 18 | pages = 10131–6 | date = August 2001 | pmid = 11504917 | pmc = 56927 | doi = 10.1073/pnas.181203898 | bibcode = 2001PNAS...9810131R | doi-access = free }} halorhodopsin,{{cite journal | vauthors = Kolbe M, Besir H, Essen LO, Oesterhelt D | title = Structure of the light-driven chloride pump halorhodopsin at 1.8 A resolution | journal = Science | volume = 288 | issue = 5470 | pages = 1390–6 | date = May 2000 | pmid = 10827943 | doi = 10.1126/science.288.5470.1390 | bibcode = 2000Sci...288.1390K }} as well as an Anabaena cyanobacterial sensory rhodopsin (TC# [http://www.tcdb.org/search/result.php?tc=3.E.1.1.6 3.E.1.1.6]){{cite journal | vauthors = Vogeley L, Sineshchekov OA, Trivedi VD, Sasaki J, Spudich JL, Luecke H | title = Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 A | journal = Science | volume = 306 | issue = 5700 | pages = 1390–3 | date = November 2004 | pmid = 15459346 | pmc = 5017883 | doi = 10.1126/science.1103943 | bibcode = 2004Sci...306.1390V }} and others.

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 ({{PDB2|1H2S}}).{{cite journal | vauthors = Gordeliy VI, Labahn J, Moukhametzianov R, Efremov R, Granzin J, Schlesinger R, Büldt G, Savopol T, Scheidig AJ, Klare JP, Engelhard M | display-authors = 6 | title = Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex | journal = Nature | volume = 419 | issue = 6906 | pages = 484–7 | date = October 2002 | pmid = 12368857 | doi = 10.1038/nature01109 | s2cid = 4425659 | bibcode = 2002Natur.419..484G }} Molecular and evolutionary aspects of the light-signal transduction by microbial sensory receptors have been reviewed.{{cite journal | vauthors = Inoue K, Tsukamoto T, Sudo Y | title = Molecular and evolutionary aspects of microbial sensory rhodopsins | journal = Biochimica et Biophysica Acta (BBA) - Bioenergetics | volume = 1837 | issue = 5 | pages = 562–77 | date = May 2014 | pmid = 23732219 | doi = 10.1016/j.bbabio.2013.05.005 | doi-access = free }}

Homologues include putative fungal chaperone proteins, a retinal-containing rhodopsin from Neurospora crassa,{{cite journal | vauthors = Maturana A, Arnaudeau S, Ryser S, Banfi B, Hossle JP, Schlegel W, Krause KH, Demaurex N | display-authors = 6 | title = Heme histidine ligands within gp91(phox) modulate proton conduction by the phagocyte NADPH oxidase | journal = The Journal of Biological Chemistry | volume = 276 | issue = 32 | pages = 30277–84 | date = August 2001 | pmid = 11389135 | doi = 10.1074/jbc.M010438200 | doi-access = free }} a H⁺-pumping rhodopsin from Leptosphaeria maculans, retinal-containing proton pumps isolated from marine bacteria,{{cite journal | vauthors = Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF | display-authors = 6 | title = Bacterial rhodopsin: evidence for a new type of phototrophy in the sea | journal = Science | volume = 289 | issue = 5486 | pages = 1902–6 | date = September 2000 | pmid = 10988064 | doi = 10.1126/science.289.5486.1902 | bibcode = 2000Sci...289.1902B }} a green light-activated photoreceptor in cyanobacteria that does not pump ions and interacts with a small (14 kDa) soluble transducer protein {{cite journal | vauthors = Jung KH, Trivedi VD, Spudich JL | title = Demonstration of a sensory rhodopsin in eubacteria | journal = Molecular Microbiology | volume = 47 | issue = 6 | pages = 1513–22 | date = March 2003 | pmid = 12622809 | doi = 10.1046/j.1365-2958.2003.03395.x | s2cid = 12052542 | doi-access = free }} and light-gated H⁺ channels from the green alga, Chlamydomonas reinhardtii.{{cite journal | vauthors = Nagel G, Ollig D, Fuhrmann M, Kateriya S, Musti AM, Bamberg E, Hegemann P | title = Channelrhodopsin-1: a light-gated proton channel in green algae | journal = Science | volume = 296 | issue = 5577 | pages = 2395–8 | date = June 2002 | pmid = 12089443 | doi = 10.1126/science.1072068 | s2cid = 206506942 | bibcode = 2002Sci...296.2395N }} 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.{{cite journal | vauthors = Brown LS, Dioumaev AK, Lanyi JK, Spudich EN, Spudich JL | title = Photochemical reaction cycle and proton transfers in Neurospora rhodopsin | journal = The Journal of Biological Chemistry | volume = 276 | issue = 35 | pages = 32495–505 | date = August 2001 | pmid = 11435422 | doi = 10.1074/jbc.M102652200 | doi-access = free }}{{cite journal | vauthors = Brown LS | title = Fungal rhodopsins and opsin-related proteins: eukaryotic homologues of bacteriorhodopsin with unknown functions | journal = Photochemical & Photobiological Sciences | volume = 3 | issue = 6 | pages = 555–65 | date = June 2004 | pmid = 15170485 | doi = 10.1039/b315527g | doi-access = free | bibcode = 2004PhPhS...3..555B }}

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; seven 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. The MR family is distantly related to the seven TMS LCT family ([http://www.tcdb.org/search/result.php?tc=2.A.43 TC# 2.A.43]). Representative members of MR family can be found in the [http://www.tcdb.org/search/result.php?tc=3.E.1.8 Transporter Classification Database].

{{Main|Bacteriorhodopsin}}

Bacteriorhodopsin pumps one H⁺ ion, from the cytosol to the extracellular medium, per photon absorbed. Specific transport mechanisms and pathways have been proposed.{{cite journal | vauthors = Lanyi JK, Schobert B | title = Mechanism of proton transport in bacteriorhodopsin from crystallographic structures of the K, L, M1, M2, and M2' intermediates of the photocycle | journal = Journal of Molecular Biology | volume = 328 | issue = 2 | pages = 439–50 | date = April 2003 | pmid = 12691752 | doi = 10.1016/s0022-2836(03)00263-8 }}{{cite journal | vauthors = Schobert B, Brown LS, Lanyi JK | title = Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base | journal = Journal of Molecular Biology | volume = 330 | issue = 3 | pages = 553–70 | date = July 2003 | pmid = 12842471 | doi = 10.1016/s0022-2836(03)00576-x }} 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. Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin.{{cite journal | vauthors = Royant A, Edman K, Ursby T, Pebay-Peyroula E, Landau EM, Neutze R | title = Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin | journal = Nature | volume = 406 | issue = 6796 | pages = 645–8 | date = August 2000 | pmid = 10949307 | doi = 10.1038/35020599 | s2cid = 4345380 | bibcode = 2000Natur.406..645R }}

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.{{cite journal | vauthors = Yoshimura K, Kouyama T | title = Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2 | journal = Journal of Molecular Biology | volume = 375 | issue = 5 | pages = 1267–81 | date = February 2008 | pmid = 18082767 | doi = 10.1016/j.jmb.2007.11.039 }}

File:Archaerhodopsin-3 6S6C.gif

{{Main|Archaerhodopsin}}

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. 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.{{cite journal | vauthors = Flytzanis NC, Bedbrook CN, Chiu H, Engqvist MK, Xiao C, Chan KY, Sternberg PW, Arnold FH, Gradinaru V | display-authors = 6 | title = Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons | journal = Nature Communications | volume = 5 | pages = 4894 | date = September 2014 | pmid = 25222271 | pmc = 4166526 | doi = 10.1038/ncomms5894 | bibcode = 2014NatCo...5.4894F }}

{{Main|Channelrhodopsin}}

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. Based on this phenotype, Chop1 could be assigned to [http://www.tcdb.org/search/result.php?tc=1.A 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.

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.{{cite journal | vauthors = Nagel G, Szellas T, Huhn W, Kateriya S, Adeishvili N, Berthold P, Ollig D, Hegemann P, Bamberg E | display-authors = 6 | title = Channelrhodopsin-2, a directly light-gated cation-selective membrane channel | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 100 | issue = 24 | pages = 13940–5 | date = November 2003 | pmid = 14615590 | pmc = 283525 | doi = 10.1073/pnas.1936192100 | bibcode = 2003PNAS..10013940N | doi-access = free }} 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.{{cite journal | vauthors = Lórenz-Fonfría VA, Resler T, Krause N, Nack M, Gossing M, Fischer von Mollard G, Bamann C, Bamberg E, Schlesinger R, Heberle J | display-authors = 6 | title = Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 110 | issue = 14 | pages = E1273-81 | date = April 2013 | pmid = 23509282 | pmc = 3619329 | doi = 10.1073/pnas.1219502110 | bibcode = 2013PNAS..110E1273L | doi-access = free }}

{{Main|Halorhodopsin}}

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.

A marine bacterial rhodopsin has been reported to function as a proton pump.{{citation needed|date=February 2025}} 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.{{citation needed|date=February 2025}}

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

:H⁺ (in) + hν → H⁺ (out).

That for halorhodopsin is:

:Cl⁻ (out) + hν → Cl⁻ (in).

• Bacteriorhodopsin
• Proteorhodopsin
• Opsin

{{Reflist|30em}}

{{Portal bar|Biology|border=no}}

Category:Sensory receptors

Category:Biological pigments

Category:Protein families

Category:Membrane proteins

Category:Transmembrane proteins

Category:Transmembrane transporters

Category:Transport proteins

Category:Integral membrane proteins

ru:Бактериородопсин