Proteorhodopsin (PR or pRhodopsin) belongs to the

family Family (from ) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). It forms the basis for social order. Ideally, families offer predictabili ...

bacterial Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the ...

transmembrane 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 u ...

rhodopsins Rhodopsin, also known as visual purple, is a protein encoded by the ''RHO'' gene and a G-protein-coupled receptor (GPCR). It is a light-sensitive receptor protein that triggers visual phototransduction in rod cells. Rhodopsin mediates dim li ...

( retinylidene proteins). In 1971, the first

microbial A microorganism, or microbe, is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells. The possible existence of unseen microbial life was suspected from antiquity, with an early attestation in ...

rhodopsin Rhodopsin, also known as visual purple, is a protein encoded by the ''RHO'' gene and a G-protein-coupled receptor (GPCR). It is a light-sensitive receptor protein that triggers visual phototransduction in rod cells. Rhodopsin mediates dim ...

Bacteriorhodopsin 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 res ...

was discovered in

archea Archaea ( ) is a domain of organisms. Traditionally, Archaea only included its prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even though the domain Archaea cladis ...

domain by Dieter Oesterhelt and Walther Stoeckenius. Later in 2000, the first

was discovered by Oded Béjà and

Edward DeLong Edward Francis DeLong (born 1958), is a marine microbiologist and professor in the Department of Oceanography at the University of Hawaii, Manoa, and is considered a pioneer in the field of metagenomics. He is best known for his discovery of the ...

. The Proteorhodopsin is widely expressed in various type of

aquatic habitats Marine biology is the scientific study of the biology of marine life, organisms that inhabit the sea. Given that in biology many phyla, families and genera have some species that live in the sea and others that live on land, marine biology clas ...

. It functions as

light Light, visible light, or visible radiation is electromagnetic radiation that can be visual perception, perceived by the human eye. Visible light spans the visible spectrum and is usually defined as having wavelengths in the range of 400– ...

-driven

proton pumps A proton pump is an integral membrane protein pump that builds up a proton gradient across a biological membrane. Proton pumps catalyze the following reaction: : n one side of a biological membrane/sub> + energy n the other side of the mem ...

with the help of

retinal Retinal (also known as retinaldehyde) 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). Some microorganisms use ret ...

chromophore A chromophore is the part of a molecule responsible for its color. The word is derived . The color that is seen by our eyes is that of the light not Absorption (electromagnetic radiation), absorbed by the reflecting object within a certain wavele ...

at the

active site In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the ''binding s ...

. The light-driven

proton pump A proton pump is an integral membrane protein pump that builds up a proton gradient across a biological membrane. Proton pumps catalyze the following reaction: : n one side of a biological membrane/sub> + energy n the other side of the m ...

gives

bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

energy in the form of

adenosine triphosphate Adenosine triphosphate (ATP) is a nucleoside triphosphate that provides energy to drive and support many processes in living cell (biology), cells, such as muscle contraction, nerve impulse propagation, and chemical synthesis. Found in all known ...

(ATP).

Discovery

Efforts by Oded Béjà from

research group in pioneering

bacterial artificial chromosome A bacterial artificial chromosome (BAC) is a DNA construct, based on a functional fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually '' E. coli''. F-plasmids play a crucial role because they contain partiti ...

metagenomics Metagenomics is the study of all genetics, genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential. Metagenomics has allowed researchers to profile the mic ...

analysis led the discovery of pRhodopsin in bacteria domain. It was first detected in uncultured

gammaproteobacteria ''Gammaproteobacteria'' is a class of bacteria in the phylum ''Pseudomonadota'' (synonym ''Proteobacteria''). It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. Several medically, ecologically, and scienti ...

ribotype group SAR86 at

Monterey Bay Monterey Bay is a bay of the Pacific Ocean located on the coast of the U.S. state of California, south of the San Francisco Bay Area. San Francisco itself is further north along the coast, by about 75 miles (120 km), accessible via California S ...

water column The (oceanic) water column is a concept used in oceanography to describe the physical (temperature, salinity, light penetration) and chemical ( pH, dissolved oxygen, nutrient salts) characteristics of seawater at different depths for a defined ...

in 2000. Oded Béjà observed the

sequence similarity Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speci ...

between SAR86 pRhodopsin and bacteriorodopsin (a light driven

in haloarchea)

open reading frame In molecular biology, reading frames are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible reading frames ...

. To further established pRhodopsin function as

-based light-driven

, he expressed pRhodopsin

Escherichia coli ''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...

system A system is a group of interacting or interrelated elements that act according to a set of rules to form a unified whole. A system, surrounded and influenced by its open system (systems theory), environment, is described by its boundaries, str ...

. Before the discovery of

Proteorhodpsin, it was understood that light driven

active transport In cellular biology, active transport is the movement of molecules or ions across a cell membrane from a region of lower concentration to a region of higher concentration—against the concentration gradient. Active transport requires cellula ...

only evolved in extreme

halophilic A halophile (from the Greek word for 'salt-loving') is an extremophile that thrives in high salt concentrations. In chemical terms, halophile refers to a Lewis acidic species that has some ability to extract halides from other chemical species. ...

archaea domain ( bacteriorodopsin,

halorhodopsin 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 approximatel ...

, and sensory rhodopsin) and animal kingdom (as a

visual The visual system is the physiological basis of visual perception (the ability to detect and process light). The system detects, transduces and interprets information concerning light within the visible range to construct an image and buil ...

Distribution

pRhodopsin is not confined to a single

species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...

and single

habitat In ecology, habitat refers to the array of resources, biotic factors that are present in an area, such as to support the survival and reproduction of a particular species. A species' habitat can be seen as the physical manifestation of its ...

. It is distributed in many

microorganisms A microorganism, or microbe, is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells. The possible existence of unseen microbial life was suspected from antiquity, with an early attestation in ...

from all over the world. pRhodopsin containing microorganisms is distributed in

Gammaproteobacteria ''Gammaproteobacteria'' is a class of bacteria in the phylum ''Pseudomonadota'' (synonym ''Proteobacteria''). It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. Several medically, ecologically, and scienti ...

Alphaproteobacteria ''Alphaproteobacteria'' or ''α-proteobacteria'', also called ''α-Purple bacteria'' in earlier literature, is a class of bacteria in the phylum '' Pseudomonadota'' (formerly "Proteobacteria"). The '' Magnetococcales'' and '' Mariprofundales'' ar ...

Betaproteobacteria ''Betaproteobacteria'' are a class of Gram-negative bacteria, and one of the six classes of the phylum '' Pseudomonadota'' (synonym Proteobacteria). Metabolism The ''Betaproteobacteria'' comprise over 75 genera and 400 species. Together, they ...

Flavobacteria The class Flavobacteriia is composed of a single class of environmental bacteria. It contains the family Flavobacteriaceae, which is the largest family in the phylum Bacteroidota. This class is widely distributed in soil, fresh, and seawater habi ...

Planctomycetes The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammoni ...

Cyanobacteria Cyanobacteria ( ) are a group of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" () refers to their bluish green (cyan) color, which forms the basis of cyanobacteri ...

Actinobacteria The Actinomycetota (or Actinobacteria) are a diverse phylum of Gram-positive bacteria with high GC content. They can be terrestrial or aquatic. They are of great importance to land flora because of their contributions to soil systems. In soil t ...

, marine

Archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...

, and different eukaryotic groups, including

fungi A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...

and

dinoflagellates The Dinoflagellates (), also called Dinophytes, are a monophyletic group of single-celled eukaryotes constituting the phylum Dinoflagellata and are usually considered protists. Dinoflagellates are mostly marine plankton, but they are also commo ...

. pRhodopsin containing microorganisms are habited in

marine environments A marine habitat is a habitat that supports marine life. Marine life depends in some way on the seawater, saltwater that is in the sea (the term ''marine'' comes from the Latin ''mare'', meaning sea or ocean). A habitat is an ecological or Na ...

sea ice Sea ice arises as seawater freezes. Because ice is less density, dense than water, it floats on the ocean's surface (as does fresh water ice). Sea ice covers about 7% of the Earth's surface and about 12% of the world's oceans. Much of the world' ...

brackish Brackish water, sometimes termed brack water, is water occurring in a natural environment that has more salinity than freshwater, but not as much as seawater. It may result from mixing seawater (salt water) and fresh water together, as in estuari ...

environments,

fresh water Fresh water or freshwater is any naturally occurring liquid or frozen water containing low concentrations of dissolved salt (chemistry), salts and other total dissolved solids. The term excludes seawater and brackish water, but it does include ...

lakes and on high

mountains A mountain is an elevated portion of the Earth's crust, generally with steep sides that show significant exposed bedrock. Although definitions vary, a mountain may differ from a plateau in having a limited summit area, and is usually higher ...

. In the

marine environment A marine habitat is a habitat that supports marine life. Marine life depends in some way on the saltwater that is in the sea (the term ''marine'' comes from the Latin ''mare'', meaning sea or ocean). A habitat is an ecological or environmen ...

, pRhodopsin containing

is primarily found in

photic zone The photic zone (or euphotic zone, epipelagic zone, or sunlight zone) is the uppermost layer of a body of water that receives sunlight, allowing phytoplankton to perform photosynthesis. It undergoes a series of physical, chemical, and biological ...

Protein Structure

The

topology Topology (from the Greek language, Greek words , and ) is the branch of mathematics concerned with the properties of a Mathematical object, geometric object that are preserved under Continuous function, continuous Deformation theory, deformat ...

and

residues for proton transporting retinylidene proteins was first characterized in

bacteriorhodopsin 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 res ...

. The pRhodopsin

and

residues are conserved to

. pRhodopsin is a seven

α-helices An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of l ...

that form a pocket in which

( vitamin A aldehyde) is covalently linked to

ligand In coordination chemistry, a ligand is an ion or molecule with a functional group that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's el ...

binding domain In molecular biology, binding domain is a protein domain which binds to a specific atom or molecule, such as calcium or DNA. A protein domain is a part of a protein sequence and a tertiary structure that can change or evolve, function, and live ...

, as a

protonated In chemistry, protonation (or hydronation) is the adding of a proton (or hydron, or hydrogen cation), usually denoted by H+, to an atom, molecule, or ion, forming a conjugate acid. (The complementary process, when a proton is removed from a Br� ...

schiff base In organic chemistry, a Schiff base (named after Hugo Schiff) is a compound with the general structure ( = alkyl or aryl, but not hydrogen). They can be considered a sub-class of imines, being either secondary ketimines or secondary aldim ...

, to a

lysine Lysine (symbol Lys or K) is an α-amino acid that is a precursor to many proteins. Lysine contains an α-amino group (which is in the protonated form when the lysine is dissolved in water at physiological pH), an α-carboxylic acid group ( ...

in the seventh

α-helix An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the Protein secondary structure, secondary structure of proteins. It is al ...

. At

ground state The ground state of a quantum-mechanical system is its stationary state of lowest energy; the energy of the ground state is known as the zero-point energy of the system. An excited state is any state with energy greater than the ground state ...

the

is all-trans configuration. When

visible light Light, visible light, or visible radiation is electromagnetic radiation that can be perceived by the human eye. Visible light spans the visible spectrum and is usually defined as having wavelengths in the range of 400–700 nanometres (nm ...

illuminates on pRhodopsin, the all-trans

molecule absorbs

light energy In physics, and in particular as measured by radiometry, radiant energy is the energy of electromagnetic and gravitational radiation. As energy, its SI unit is the joule (J). The quantity of radiant energy may be calculated by integrating radian ...

and uses it to isomerize into 13-cis configuration. This triggers a sequence of

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

conformational changes including several proton transfer reactions against

concentration gradient Fick's laws of diffusion describe diffusion and were first posited by Adolf Fick in 1855 on the basis of largely experimental results. They can be used to solve for the diffusion coefficient, . Fick's first law can be used to derive his second ...

, generating a

proton motive force Chemiosmosis is the movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient. An important example is the formation of adenosine triphosphate (ATP) by the movement of hydrogen ions (H+) across a membra ...

Function

Light Light, visible light, or visible radiation is electromagnetic radiation that can be visual perception, perceived by the human eye. Visible light spans the visible spectrum and is usually defined as having wavelengths in the range of 400– ...

-activated proteorhodopsin

pumps A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action, typically converted from electrical energy into hydraulic or pneumatic energy. Mechanical pumps serve in a wide range of applications such ...

protons A proton is a stable subatomic particle, symbol , H+, or 1H+ with a positive electric charge of +1 ''e'' ( elementary charge). Its mass is slightly less than the mass of a neutron and approximately times the mass of an electron (the pro ...

outwardly, increasing the

across the

cell membrane The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a cell from the outside environment (the extr ...

Protons A proton is a stable subatomic particle, symbol , H+, or 1H+ with a positive electric charge of +1 ''e'' ( elementary charge). Its mass is slightly less than the mass of a neutron and approximately times the mass of an electron (the pro ...

can then reenter the cell through the

ATP synthase ATP synthase is an enzyme that catalyzes the formation of the energy storage molecule adenosine triphosphate (ATP) using adenosine diphosphate (ADP) and inorganic phosphate (Pi). ATP synthase is a molecular machine. The overall reaction catalyzed ...

complex, powering the

synthesis Synthesis or synthesize may refer to: Science Chemistry and biochemistry *Chemical synthesis, the execution of chemical reactions to form a more complex molecule from chemical precursors **Organic synthesis, the chemical synthesis of organi ...

of ATP. Proteorhodopsin thus allows

cells Cell most often refers to: * Cell (biology), the functional basic unit of life * Cellphone, a phone connected to a cellular network * Clandestine cell, a penetration-resistant form of a secret or outlawed organization * Electrochemical cell, a d ...

to harvest

energy Energy () is the physical quantity, quantitative physical property, property that is transferred to a physical body, body or to a physical system, recognizable in the performance of Work (thermodynamics), work and in the form of heat and l ...

and convert it into usable

chemical energy Chemical energy is the energy of chemical substances that is released when the substances undergo a chemical reaction and transform into other substances. Some examples of storage media of chemical energy include batteries, Schmidt-Rohr, K. (20 ...

without the involvement of

chlorophyll Chlorophyll is any of several related green pigments found in cyanobacteria and in the chloroplasts of algae and plants. Its name is derived from the Greek words (, "pale green") and (, "leaf"). Chlorophyll allows plants to absorb energy ...

-based

photosystems Photosystems are functional and structural units of protein complexes involved in photosynthesis. Together they carry out the primary photochemistry of photosynthesis: the absorption of light and the transfer of energy and electrons. Photosystems ...

Microbes A microorganism, or microbe, is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells. The possible existence of unseen microbial life was suspected from antiquity, with an early attestation in ...

containing proteorhodopsin are considered

phototrophs Phototrophs () are organisms that carry out photon capture to produce complex organic compounds (e.g. carbohydrates) and acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconce ...

due to its functionality as a light-sensitive

. Different

variants Variant may refer to: Arts and entertainment * ''Variant'' (magazine), a former British cultural magazine * Variant cover, an issue of comic books with varying cover art * ''Variant'' (novel), a novel by Robison Wells * " The Variant", 2021 epis ...

of proteorhodopsin are spectrally tuned to absorb specific

wavelengths In physics and mathematics, wavelength or spatial period of a wave or periodic function is the distance over which the wave's shape repeats. In other words, it is the distance between consecutive corresponding points of the same '' phase'' on ...

, such as

green Green is the color between cyan and yellow on the visible spectrum. It is evoked by light which has a dominant wavelength of roughly 495570 nm. In subtractive color systems, used in painting and color printing, it is created by a com ...

blue Blue is one of the three primary colours in the RYB color model, RYB colour model (traditional colour theory), as well as in the RGB color model, RGB (additive) colour model. It lies between Violet (color), violet and cyan on the optical spe ...

. These

adaptations In biology, adaptation has three related meanings. Firstly, it is the dynamic evolutionary process of natural selection that fits organisms to their environment, enhancing their evolutionary fitness. Secondly, it is a state reached by the p ...

allow

organisms An organism is any living thing that functions as an individual. Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have been pr ...

to occupy distinct

ecological niches In ecology, a niche is the match of a species to a specific environmental condition. Three variants of ecological niche are described by It describes how an organism or population responds to the distribution of resources and competitors (for e ...

based on

availability at different

depths. These

functional Functional may refer to: * Movements in architecture: ** Functionalism (architecture) ** Form follows function * Functional group, combination of atoms within molecules * Medical conditions without currently visible organic basis: ** Functional s ...

advantages make proteorhodopsin a key component in the marine

energy budget An energy budget is a balance sheet of energy income against expenditure. It is studied in the field of Energetics which deals with the study of energy transfer and transformation from one form to another. Calories and joules are the basic units ...

Genetic engineering

If the

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

for proteorhodopsin is inserted into ''

E. coli ''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escherichia'' that is commonly foun ...

'' and retinal is given to these modified

, then they will incorporate the

pigment A pigment is a powder used to add or alter color or change visual appearance. Pigments are completely or nearly solubility, insoluble and reactivity (chemistry), chemically unreactive in water or another medium; in contrast, dyes are colored sub ...

into their

and will pump H+ in the presence of

. This functionality can be used to acidify a

vesicle Vesicle may refer to: ; In cellular biology or chemistry * Vesicle (biology and chemistry), a supramolecular assembly of lipid molecules, like a cell membrane * Synaptic vesicle ; In human embryology * Vesicle (embryology), bulge-like features ...

type

organelle In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as Organ (anatomy), organs are to th ...

Gallery

File:Proteorhodopsin Cartoon Visualization E.Vitureira 4-16.png, Holoenzyme (Green) with helices A-G labeled (purple) as well as Retinal ligand (orange) File:PR surface visualization - ELViture April 2016.png, Surface visualization of Proteorhodopsin showing terminals File: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. File: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

References

{{Optogenetics Bacterial proteins Integral membrane proteins Photosynthesis