Phycoerythrin, alpha/beta chain | |||||||||
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Identifiers | |||||||||
Symbol | Phycoerythr_ab | ||||||||
Pfam | PF02972 | ||||||||
InterPro | IPR004228 | ||||||||
SCOP2 | 1qgw / SCOPe / SUPFAM | ||||||||
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Phycoerythrin (PE) is a red protein-pigment complex from the light-harvesting phycobiliprotein family, present in cyanobacteria, [1] red algae [2] and cryptophytes, [3] accessory to the main chlorophyll pigments responsible for photosynthesis.The red pigment is due to the prosthetic group, phycoerythrobilin, which gives phycoerythrin its red color. [4]
Like all phycobiliproteins, it is composed of a protein part covalently binding chromophores called phycobilins. In the phycoerythrin family, the most known phycobilins are: phycoerythrobilin, the typical phycoerythrin acceptor chromophore. Phycoerythrobilin is a linear tetrapyrrole molecule found in cyanobacteria, red algae, and cryptomonads. Together with other bilins such as phycocyanobilin it serves as a light-harvesting pigment in the photosynthetic light-harvesting structures of cyanobacteria called phycobilisomes. [5] Phycoerythrins are composed of (αβ) monomers, usually organised in a disk-shaped trimer (αβ)3 or hexamer (αβ)6 (second one is the functional unit of the antenna rods). These typical complexes also contain a third type of subunit, the γ chain. [2]
Phycobiliproteins are part of huge light harvesting antennae protein complexes called phycobilisomes. In red algae they are anchored to the stromal side of thylakoid membranes of chloroplasts, whereas in cryptophytes phycobilisomes are reduced and (phycobiliprotein 545 PE545 molecules here) are densely packed inside the lumen of thylakoides. [3] [7]
Phycobiliproteins have many practical application to them including imperative properties like hepato-protective, anti-oxidants, anti-inflammatory and anti-aging activity of PBPs enable their use in food, cosmetics, pharmaceutical and biomedical industries. PBPs have been also noted to show beneficial effect in therapeutics of some disease like Alzheimer and cancer. [8]
Phycoerythrin is an accessory pigment to the main chlorophyll pigments responsible for photosynthesis. The light energy is captured by phycoerythrin and is then passed on to the reaction centre chlorophyll pair, most of the time via the phycobiliproteins phycocyanin and allophycocyanin.
Phycoerythrins except phycoerythrin 545 (PE545) are composed of (αβ) monomers assembled into disc-shaped (αβ)6 hexamers or (αβ)3 trimers with 32 or 3 symmetry and enclosing central channel. In phycobilisomes (PBS) each trimer or hexamer contains at least one linker protein located in central channel. B-phycoerythrin (B-PE) and R-phycoerythrin (R-PE) from red algae in addition to α and β chains have a third, γ subunit contributing both linker and light-harvesting functions, because it bears chromophores. [2]
R-phycoerythrin is predominantly produced by red algae. The protein is made up of at least three different subunits and varies according to the species of algae that produces it. The subunit structure of the most common R-PE is (αβ)6γ. The α subunit has two phycoerythrobilins (PEB), the β subunit has 2 or 3 PEBs and one phycourobilin (PUB), while the different gamma subunits are reported to have 3 PEB and 2 PUB (γ1) or 1 or 2 PEB and 1 PUB (γ2). The molecular weight of R-PE is 250,000 daltons.
Crystal structures available in the Protein Data Bank [12] contain in one (αβ)2 or (αβγ)2 asymmetric unit of different phycoerythrins:
Chromophore or other non-protein molecule | Phycoerythrin | Chain | |||
---|---|---|---|---|---|
PE545 | B-PE | R-PE | other types | ||
Bilins | 8 | 10 | 10 | 10 | α and β |
- Phycoerythrobilin (PEB) | 6 | 10 | 0 or 8 | 8 | β (PE545) or α and β |
- 15,16-dihydrobiliverdin (DBV) | 2 | — | — | — | α (-3 and -2) |
- Phycocyanobilin (CYC) | — | — | 8 or 7 or 0 | — | α and β |
- Biliverdine IX alpha (BLA) | — | — | 0 or 1 | — | α |
- Phycourobilin (PUB) | — | — | 2 | 2 | β |
5-hydroxylysine (LYZ) | 1 or 2 | — | — | — | α (-3 or -3 and -2) |
N-methyl asparagine (MEN) | 2 | 2 | 0 or 2 | 2 | β |
Sulfate ion SO42− (SO4) | — | 5 or 1 | 0 or 2 | — | α or α and β |
Chloride ion Cl− (CL) | 1 | — | — | — | β |
Magnesium ion Mg2+ (MG) | 2 | — | — | — | α-3 and β |
inspected PDB files | 1XG0 1XF6 1QGW | 3V57 3V58 | 1EYX 1LIA 1B8D | 2VJH |
The assumed biological molecule of phycoerythrin 545 (PE545) is (αβ)2 or rather (α3β)(α2β). The numbers 2 and 3 after the α letters in second formula are part of chain names here, not their counts. The synonym cryptophytan name of α3 chain is α1 chain.
The largest assembly of B-phycoerythrin (B-PE) is (αβ)3 trimer [9] [10] . However, preparations from red algae yield also (αβ)6 hexamer [2] . In case of R-phycoerythrin (R-PE) the largest assumed biological molecule here is (αβγ)6, (αβγ)3(αβ)3 or (αβ)6 dependently on publication, for other phycoerythrin types (αβ)6. These γ chains from the Protein Data Bank are very small and consist only of three or six recognizable amino acids [15] [16] , whereas described at the beginning of this section linker γ chain is large (for example 277 amino acid long 33 kDa in case of γ33 from red algae Aglaothamnion neglectum ) [17] [2] . This is because the electron density of the gamma-polypeptide is mostly averaged out by its threefold crystallographic symmetry and only a few amino acids can be modeled [15] [16] [18] [19] .
For (αβγ)6, (αβ)6 or (αβγ)3(αβ)3 the values from the table should be simply multiplied by 3, (αβ)3 contain intermediate numbers of non-protein molecules. (this non sequitur needs to be corrected)
In phycoerythrin PE545 above, one α chain (-2 or -3) binds one molecule of billin, in other examples it binds two molecules. The β chain always binds to three molecules. The small γ chain binds to none.
Two molecules of N-methyl asparagine are bound to the β chain, one 5-hydroxylysine to α (-3 or -2), one Mg2+ to α-3 and β, one Cl− to β, 1–2 molecules of SO2−
4 to α or β.
Below is sample crystal structure of R-phycoerythrin from Protein Data Bank:
Absorption peaks in the visible light spectrum are measured at 495 and 545/566 nm, depending on the chromophores bound and the considered organism. A strong emission peak exists at 575 ± 10 nm. (Phycoerythrin absorbs slightly blue-green/yellowish light and emits slightly orange-yellow light.)
Property | Value |
---|---|
Absorption maximum | 565 nm |
Additional Absorption peak | 498 nm |
Emission maximum | 573 nm |
Extinction Coefficient (ε) | 1.96×106 M−1 cm−1 |
Quantum Yield (QY) | 0.84 |
Brightness (ε × QY) | 1.65×106 M−1 cm−1 |
PEB and DBV bilins in PE545 absorb in the green spectral region too, with maxima at 545 and 569 nm respectively. The fluorescence emission maximum is at 580 nm. [3]
As mentioned above, phycoerythrin can be found in a variety of algal species. As such, there can be variation in the efficiency of absorbance and emission of light required for facilitation of photosynthesis. This could be a result of the depth in the water column that a specific alga typically resides and a consequent need for greater or less efficiency of the accessory pigments.
With advances in imaging and detection technology which can avoid rapid photobleaching, protein fluorophores have become a viable and powerful tool for researchers in fields such as microscopy, microarray analysis and Western blotting. In light of this, it may be beneficial for researchers to screen these variable R-phycoerythrins to determine which one is most appropriate for their particular application. Even a small increase in fluorescent efficiency could reduce background noise and lower the rate of false-negative results.
R-Phycoerythrin (also known as PE or R-PE) is useful in the laboratory as a fluorescence-based indicator for the presence of cyanobacteria and for labeling antibodies, most often for flow cytometry. Its also used in microarray assays, ELISAs, and other applications that require high sensitivity but not photostability. [20] Its use is limited in immunofluorescence microscopy due to its rapid photobleaching characteristics. There are also other types of phycoerythrins, such as B-phycoerythrin, which have slightly different spectral properties. B-Phycoerythrin absorbs strongly at about 545 nm (slightly yellowish green) and emits strongly at 572 nm (yellow) instead and could be better suited for some instruments. B-Phycoerythrin may also be less "sticky" than R-phycoerythrin and contributes less to background signal due to nonspecific binding in certain applications.[ citation needed ] However, R-PE is much more commonly available as an antibody conjugate. Phycoerythrin (PE, λA max = 540–570 nm; λF max = 575–590 nm) [8]
R-Phycoerythrin and B-phycoerythrin are among the brightest fluorescent dyes ever identified.
Integrins are transmembrane receptors that help cell–cell and cell–extracellular matrix (ECM) adhesion. Upon ligand binding, integrins activate signal transduction pathways that mediate cellular signals such as regulation of the cell cycle, organization of the intracellular cytoskeleton, and movement of new receptors to the cell membrane. The presence of integrins allows rapid and flexible responses to events at the cell surface.
The cryptomonads are a group of algae, most of which have plastids. They are traditionally considered a division of algae among phycologists, under the name of Cryptophyta. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10–50 μm in size and flattened in shape, with an anterior groove or pocket. At the edge of the pocket there are typically two slightly unequal flagella. Some may exhibit mixotrophy. They are classified as clade Cryptomonada, which is divided into two classes: heterotrophic Goniomonadea and phototrophic Cryptophyceae. The two groups are united under three shared morphological characteristics: presence of a periplast, ejectisomes with secondary scroll, and mitochondrial cristae with flat tubules. Genetic studies as early as 1994 also supported the hypothesis that Goniomonas was sister to Cryptophyceae. A study in 2018 found strong evidence that the common ancestor of Cryptomonada was an autotrophic protist.
Cryptomonas is the name-giving genus of the Cryptomonads established by German biologist Christian Gottfried Ehrenberg in 1831. The algae are common in freshwater habitats and brackish water worldwide and often form blooms in greater depths of lakes. The cells are usually brownish or greenish in color and are characteristic of having a slit-like furrow at the anterior. They are not known to produce any toxins. They are used to feed small zooplankton, which is the food source for small fish in fish farms. Many species of Cryptomonas can only be identified by DNA sequencing. Cryptomonas can be found in several marine ecosystems in Australia and South Korea.
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.
The glucose oxidase enzyme also known as notatin is an oxidoreductase that catalyses the oxidation of glucose to hydrogen peroxide and D-glucono-δ-lactone. This enzyme is produced by certain species of fungi and insects and displays antibacterial activity when oxygen and glucose are present.
Accessory pigments are light-absorbing compounds, found in photosynthetic organisms, that work in conjunction with chlorophyll a. They include other forms of this pigment, such as chlorophyll b in green algal and vascular ("higher") plant antennae, while other algae may contain chlorophyll c or d. In addition, there are many non-chlorophyll accessory pigments, such as carotenoids or phycobiliproteins, which also absorb light and transfer that light energy to photosystem chlorophyll. Some of these accessory pigments, in particular the carotenoids, also serve to absorb and dissipate excess light energy, or work as antioxidants. The large, physically associated group of chlorophylls and other accessory pigments is sometimes referred to as a pigment bed.
Phycocyanin is a pigment-protein complex from the light-harvesting phycobiliprotein family, along with allophycocyanin and phycoerythrin. It is an accessory pigment to chlorophyll. All phycobiliproteins are water-soluble, so they cannot exist within the membrane like carotenoids can. Instead, phycobiliproteins aggregate to form clusters that adhere to the membrane called phycobilisomes. Phycocyanin is a characteristic light blue color, absorbing orange and red light, particularly 620 nm, and emits fluorescence at about 650 nm. Allophycocyanin absorbs and emits at longer wavelengths than phycocyanin C or phycocyanin R. Phycocyanins are found in cyanobacteria. Phycobiliproteins have fluorescent properties that are used in immunoassay kits. Phycocyanin is from the Greek phyco meaning “algae” and cyanin is from the English word “cyan", which conventionally means a shade of blue-green and is derived from the Greek “kyanos" which means a somewhat different color: "dark blue". The product phycocyanin, produced by Aphanizomenon flos-aquae and Spirulina, is for example used in the food and beverage industry as the natural coloring agent 'Lina Blue' or 'EXBERRY Shade Blue' and is found in sweets and ice cream. In addition, fluorescence detection of phycocyanin pigments in water samples is a useful method to monitor cyanobacteria biomass.
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Phycoerythrocyanin is a kind of phycobiliprotein, magenta chromoprotein involved in photosynthesis of some Cyanobacteria. This chromoprotein consists of alpha- and beta-subunits, generally aggregated as hexamer. Alpha-phycoerythrocyanin contains a phycoviolobilin, a violet bilin, that covalently attached at Cys-84, and beta-phycoerythrocyanin contains two phycocyanobilins, a blue bilin, that covalently attached at Cys-84 and -155, respectively. Phycoerythrocyanin is similar to phycocyanin, an important component of the light-harvesting complex (phycobilisome) of cyanobacteria and red algae.
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Biliproteins are pigment protein compounds that are located in photosynthesising organisms such as algae, and sometimes also in certain insects. They refer to any protein that contains a bilin chromophore. In plants and algae, the main function of biliproteins is to make the process of light accumulation required for photosynthesis more efficient; while in insects they play a role in growth and development. Some of their properties: including light-receptivity, light-harvesting and fluorescence have made them suitable for applications in bioimaging and as indicators; while other properties such as anti-oxidation, anti-aging and anti-inflammation in phycobiliproteins have given them potential for use in medicine, cosmetics and food technology. While research on biliproteins dates back as far as 1950, it was hindered due to issues regarding biliprotein structure, lack of methods available for isolating individual biliprotein components, as well as limited information on lyase reactions . Research on biliproteins has also been primarily focused on phycobiliproteins; but advances in technology and methodology, along with the discovery of different types of lyases, has renewed interest in biliprotein research, allowing new opportunities for investigating biliprotein processes such as assembly/disassembly and protein folding.
Alexander Glazer was a professor of the Graduate School in the Department of Molecular and Cell Biology at the University of California, Berkeley. He had a passion for protein chemistry and structure function relationships. He also had a longstanding interest in light-harvesting complexes in cyanobacteria and red algae called phycobilisomes. He had also spent more than 10 years working on the human genome project where he has investigated methods for DNA detection and sequencing which most notably includes the development of fluorescent reagents involved in cell labeling. Most recently, he had focused his studies on issues in environmental sciences. He died on July 18, 2021, in Orinda, California
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