Small ultra red fluorescent protein (smURFP) is a class of far-red
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
evolved from a
cyanobacterial (''
Trichodesmium erythraeum'')
phycobiliprotein
Phycobiliproteins are water-soluble proteins present in cyanobacteria and certain algae ( rhodophytes, cryptomonads, glaucocystophytes). They capture light energy, which is then passed on to chlorophylls during photosynthesis. Phycobiliproteins ar ...
, α-
allophycocyanin
Allophycocyanin ("other algal blue protein"; from Greek: '' (allos)'' meaning "other", '' (phykos)'' meaning “alga”, and '' (kyanos)'' meaning "blue") is a protein from the light-harvesting phycobiliprotein family, along with phycocyanin, phyc ...
.
Native α-
allophycocyanin
Allophycocyanin ("other algal blue protein"; from Greek: '' (allos)'' meaning "other", '' (phykos)'' meaning “alga”, and '' (kyanos)'' meaning "blue") is a protein from the light-harvesting phycobiliprotein family, along with phycocyanin, phyc ...
requires an exogenous protein, known as a
lyase
In biochemistry, a lyase is an enzyme that catalyzes the breaking (an elimination reaction) of various chemical bonds by means other than hydrolysis (a substitution reaction) and oxidation, often forming a new double bond or a new ring structur ...
, to attach the
chromophore
A chromophore is the part of a molecule responsible for its color.
The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molec ...
,
phycocyanobilin
Phycocyanobilin is a blue phycobilin, i.e., a tetrapyrrole chromophore found in cyanobacteria and in the chloroplasts of red algae, glaucophytes, and some cryptomonads. Phycocyanobilin is present only in the phycobiliproteins allophycocyanin and ...
.
Phycocyanobilin
Phycocyanobilin is a blue phycobilin, i.e., a tetrapyrrole chromophore found in cyanobacteria and in the chloroplasts of red algae, glaucophytes, and some cryptomonads. Phycocyanobilin is present only in the phycobiliproteins allophycocyanin and ...
is not present in
mammal
Mammals () are a group of vertebrate animals constituting the class Mammalia (), characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or ...
ian
cells
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
. smURFP was evolved to
covalently
A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atoms ...
attach
phycocyanobilin
Phycocyanobilin is a blue phycobilin, i.e., a tetrapyrrole chromophore found in cyanobacteria and in the chloroplasts of red algae, glaucophytes, and some cryptomonads. Phycocyanobilin is present only in the phycobiliproteins allophycocyanin and ...
without a
lyase
In biochemistry, a lyase is an enzyme that catalyzes the breaking (an elimination reaction) of various chemical bonds by means other than hydrolysis (a substitution reaction) and oxidation, often forming a new double bond or a new ring structur ...
and
fluoresce
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
,
covalently
A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atoms ...
attach
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
(ubiquitous to
mammal
Mammals () are a group of vertebrate animals constituting the class Mammalia (), characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or ...
ian
cells
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
) and
fluoresce
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
,
blue-shift
In physics, a redshift is an increase in the wavelength, and corresponding decrease in the frequency and photon energy, of electromagnetic radiation (such as light). The opposite change, a decrease in wavelength and simultaneous increase in fr ...
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
to match the organic
fluorophore
A fluorophore (or fluorochrome, similarly to a chromophore) is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with sev ...
,
Cy5, and not inhibit ''
E. coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Es ...
'' growth. smURFP was found after 12 rounds of random mutagenesis and manually screening 10,000,000
bacterial colonies.
Properties
smURFP is a homodimer with
absorption and
emission maximum of 642 nm and 670 nm, respectively. A tandem dimer smURFP (TDsmURFP) was created and has similar properties to smURFP. smURFP is extremely stable with a
protein degradation
Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, ...
half-life
Half-life (symbol ) is the time required for a quantity (of substance) to reduce to half of its initial value. The term is commonly used in nuclear physics to describe how quickly unstable atoms undergo radioactive decay or how long stable ato ...
of 17 hour and 33 hour without and with
chromophore
A chromophore is the part of a molecule responsible for its color.
The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molec ...
(
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
), respectively. This is comparable to the
jellyfish
Jellyfish and sea jellies are the informal common names given to the medusa-phase of certain gelatinous members of the subphylum Medusozoa, a major part of the phylum Cnidaria. Jellyfish are mainly free-swimming marine animals with umbrella ...
-derived enhanced green fluorescent protein (
eGFP
The green fluorescent protein (GFP) is a protein that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish '' Aequor ...
)
protein degradation
Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, ...
half-life
Half-life (symbol ) is the time required for a quantity (of substance) to reduce to half of its initial value. The term is commonly used in nuclear physics to describe how quickly unstable atoms undergo radioactive decay or how long stable ato ...
of 24 hour. smURFP is extremely photostable and out performs
mCherry
mCherry is a member of the mFruits family of monomeric red fluorescent proteins (mRFPs). As a RFP, mCherry was derived from DsRed of '' Discosoma'' sea anemones unlike green fluorescent proteins (GFPs) which are often derived from '' Aequoera vic ...
and tdTomato
in living cells. The
extinction coefficient (180,000 M
−1 cm
−1) of smURFP is extremely large and has a modest
quantum yield The quantum yield (Φ) of a radiation-induced process is the number of times a specific event occurs per photon absorbed by the system.
Applications
Fluorescence spectroscopy
The fluorescence quantum yield is defined as the ratio of the numb ...
(0.18), which makes it comparable biophysical brightness to
eGFP
The green fluorescent protein (GFP) is a protein that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish '' Aequor ...
and ~2-fold brighter than most red or far-red
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
s derived from
coral. Despite being a homodimer, all tested N- and C- terminal
fusions show correct cellular localization, including the difficult
fusion
Fusion, or synthesis, is the process of combining two or more distinct entities into a new whole.
Fusion may also refer to:
Science and technology Physics
*Nuclear fusion, multiple atomic nuclei combining to form one or more different atomic nucl ...
to
α-tubulin and
Lamin B1
Lamin-B1 is a protein that in humans is encoded by the ''LMNB1'' gene.
The nuclear lamina consists of a two-dimensional matrix of proteins located next to the inner nuclear membrane. The lamin family of proteins make up the matrix and are highly ...
(
Figure).
smURFP is named after
the Smurfs
''The Smurfs'' (french: Les Schtroumpfs; nl, De Smurfen) is a Belgian comic franchise centered on a fictional colony of small, blue, humanoid creatures who live in mushroom-shaped houses in the forest. ''The Smurfs'' was first created and i ...
, due to its light blue appearance in white light.
An Excel sheet of the smURFP absorbance, excitation, and emission spectra can be downloade
here The crystal structure of a smURFP mutant () was published i
Fuenzalida-Werner et al A 2020 review discusses recent applications of smURFP as a genetically encoded or exogenous probe for ''in vivo'' imaging and discusses problems with
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
availability.
smURFP used as nanoparticles, exogenous probes, and ''in vitro'' assays
Free smURFP is 2-3 nm in diameter. smURFP
nanoparticle
A nanoparticle or ultrafine particle is usually defined as a particle of matter that is between 1 and 100 nanometres (nm) in diameter. The term is sometimes used for larger particles, up to 500 nm, or fibers and tubes that are less than 10 ...
s of ~10-14 nm diameter can be synthesized in an oil and water
emulsion
An emulsion is a mixture of two or more liquids that are normally immiscible (unmixable or unblendable) owing to liquid-liquid phase separation. Emulsions are part of a more general class of two-phase systems of matter called colloids. Although ...
and remain
fluorescent
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
. These
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
nanoparticle
A nanoparticle or ultrafine particle is usually defined as a particle of matter that is between 1 and 100 nanometres (nm) in diameter. The term is sometimes used for larger particles, up to 500 nm, or fibers and tubes that are less than 10 ...
s are stable in living mice and useful for
non-invasive
A medical procedure is defined as ''non-invasive'' when no break in the skin is created and there is no contact with the mucosa, or skin break, or internal body cavity beyond a natural or artificial body orifice. For example, deep palpation and pe ...
tumor
A neoplasm () is a type of abnormal and excessive growth of tissue. The process that occurs to form or produce a neoplasm is called neoplasia. The growth of a neoplasm is uncoordinated with that of the normal surrounding tissue, and persists ...
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
imaging.
Purified smURFP survives
ultrasound
Ultrasound is sound waves with frequencies higher than the upper audible limit of human hearing. Ultrasound is not different from "normal" (audible) sound in its physical properties, except that humans cannot hear it. This limit varies ...
and
fixation to allow
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
imaging of
macromolecule
A macromolecule is a very large molecule important to biophysical processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. The ...
delivery by
ultrasound
Ultrasound is sound waves with frequencies higher than the upper audible limit of human hearing. Ultrasound is not different from "normal" (audible) sound in its physical properties, except that humans cannot hear it. This limit varies ...
into
corneas
The cornea is the transparent front part of the eye that covers the iris, pupil, and anterior chamber. Along with the anterior chamber and lens, the cornea refracts light, accounting for approximately two-thirds of the eye's total optical powe ...
.
Free smURFP, purified protein and not genetically encoded, can be encapsulated into
virus
A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea.
Since Dmitri Ivanovsky's ...
es and used for
non-invasive
A medical procedure is defined as ''non-invasive'' when no break in the skin is created and there is no contact with the mucosa, or skin break, or internal body cavity beyond a natural or artificial body orifice. For example, deep palpation and pe ...
,
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
imaging of
biodistribution Biodistribution is a method of tracking where compounds of interest travel in an experimental animal or human subject. For example, in the development of new compounds for PET (positron emission tomography) scanning, a radioactive isotope is chemic ...
in living mice.
smURFP covalently attaches
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
to turn on
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
and is inherently a
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
sensor. Researchers showed purified smURFP has a limit of detection of 0.4 nM for
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
in
human
Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, an ...
serum. smURFP allows for the creation of ''
in vitro
''In vitro'' (meaning in glass, or ''in the glass'') studies are performed with microorganisms, cells, or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in biology and ...
'' assays to detect
enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. ...
activity. An
assay
An assay is an investigative (analytic) procedure in laboratory medicine, mining, pharmacology, environmental biology and molecular biology for qualitatively assessing or quantitatively measuring the presence, amount, or functional activity of a ...
was developed for
thrombin
Thrombin (, ''fibrinogenase'', ''thrombase'', ''thrombofort'', ''topical'', ''thrombin-C'', ''tropostasin'', ''activated blood-coagulation factor II'', ''blood-coagulation factor IIa'', ''factor IIa'', ''E thrombin'', ''beta-thrombin'', ''gamma- ...
with a detection range of 1.07 aM–0.01 mM and a limit of detection of 0.2 aM.
Tandem dimer smURFP (TDsmURFP) was used as an exogenous fluorescent marker to label the seven-
transmembrane receptor
Cell surface receptors (membrane receptors, transmembrane receptors) are receptors that are embedded in the plasma membrane of cells. They act in cell signaling by receiving (binding to) extracellular molecules. They are specialized integral m ...
Smoothened
Smoothened is a protein that in humans is encoded by the SMO gene. Smoothened is a Class Frizzled (Class F) G protein-coupled receptor that is a component of the hedgehog signaling pathway and is conserved from flies to humans. It is the molecu ...
(
SMO). TDsmURFP was purified from ''
E. coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Es ...
'' and attached to
SMO by
sortase
Sortase refers to a group of prokaryotic enzymes that modify surface proteins by recognizing and cleaving a carboxyl-terminal sorting signal. For most substrates of sortase enzymes, the recognition signal consists of the motif LPXTG (Leu-Pro-any ...
-mediated conjugation for
fluorescence-activated cell sorting (FACS). This novel, exogenous
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
labeling avoids screening multiple protein insertion sites, organic solvents, and chemical reactions that misfold, inactivate, or degrade proteins.
smURFP is a self-labeling protein
The small Ultra-Red Fluorescent Protein (smURFP) is a self-labeling protein like
Halo-,
SNAP-, and
CLIP
Clip or CLIP may refer to:
Fasteners
* Hair clip, a device used to hold hair together or attaching materials such as caps to the hair
* Binder clip, a device used for holding thicker materials (such as large volumes of paper) together
** Bulldog ...
-tags. The smURFP-tag accepts a
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
substrate modified on a
carboxylate
In organic chemistry, a carboxylate is the conjugate base of a carboxylic acid, (or ). It is an ion with negative charge.
Carboxylate salts are salts that have the general formula , where M is a metal and ''n'' is 1, 2,...; ''carboxylat ...
with a
polyethylene glycol
Polyethylene glycol (PEG; ) is a polyether compound derived from petroleum with many applications, from industrial manufacturing to medicine. PEG is also known as polyethylene oxide (PEO) or polyoxyethylene (POE), depending on its molecular we ...
(PEG) linker to the cargo molecule. Unlike the Halo-, SNAP-, and CLIP-tags that use the substrate to only covalently attach the cargo molecule, biliverdin is
fluorogenic
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, th ...
, and
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
is turned "on" with covalent attachment to the smURFP-tag to allow far-red fluorescence tracking of cargo molecule in living cells. Biliverdin also
quenches fluorescein
Fluorescein is an organic compound and dye based on the xanthene tricyclic structural motif, formally belonging to triarylmethine dyes family. It is available as a dark orange/red powder slightly soluble in water and alcohol. It is widely used ...
cargo to allow for imaging without substrate removal. Biliverdin modification on a single carboxylate creates a neutral molecule that passes the
outer and
nuclear membrane
The nuclear envelope, also known as the nuclear membrane, is made up of two lipid bilayer membranes that in eukaryotic cells surround the nucleus, which encloses the genetic material.
The nuclear envelope consists of two lipid bilayer membran ...
of mammalian
cells
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
.
Chromophore availability in cells and mice
Despite showing comparable biophysical brightness to
eGFP
The green fluorescent protein (GFP) is a protein that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish '' Aequor ...
when purified
protein was normalized, this was not seen in living
cells
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
. This suggested there was not enough
chromophore
A chromophore is the part of a molecule responsible for its color.
The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molec ...
(
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
) within
cells
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
. Addition of
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
increased
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
, but smURFP with
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
was not comparable to
eGFP
The green fluorescent protein (GFP) is a protein that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish '' Aequor ...
.
Biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
has two
carboxylate
In organic chemistry, a carboxylate is the conjugate base of a carboxylic acid, (or ). It is an ion with negative charge.
Carboxylate salts are salts that have the general formula , where M is a metal and ''n'' is 1, 2,...; ''carboxylat ...
s at neutral
pH and this is inhibiting cellular entry
Biliverdin dimethyl esteris a more
hydrophobic
In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water.
Hydrophobic molecules tend to be nonpolar and, t ...
analog and readily crosses the cellular
membrane. smURFP wit
biliverdin dimethyl estershows comparable fluorescence to
eGFP
The green fluorescent protein (GFP) is a protein that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish '' Aequor ...
in
cells
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
and is brighter than
bacterial
phytochrome
Phytochromes are a class of photoreceptor in plants, bacteria and fungi used to detect light. They are sensitive to light in the red and far-red region of the visible spectrum and can be classed as either Type I, which are activated by far-re ...
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
s.
In mice, smURFP
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
is visible in
HT1080 HT1080 is a fibrosarcoma cell line which has been used extensively in biomedical research. The cell line was created from tissue taken in a biopsy of a fibrosarcoma present in a 35-year-old human male. The patient who supplied the sample had not un ...
tumor
A neoplasm () is a type of abnormal and excessive growth of tissue. The process that occurs to form or produce a neoplasm is called neoplasia. The growth of a neoplasm is uncoordinated with that of the normal surrounding tissue, and persists ...
xenografts
Xenotransplantation (''xenos-'' from the Greek meaning "foreign" or strange), or heterologous transplant, is the transplantation of living cells, tissues or organs from one species to another. Such cells, tissues or organs are called xenograft ...
without exogenous
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
, but
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
is less than
coral-derived red
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
s,
mCherry
mCherry is a member of the mFruits family of monomeric red fluorescent proteins (mRFPs). As a RFP, mCherry was derived from DsRed of '' Discosoma'' sea anemones unlike green fluorescent proteins (GFPs) which are often derived from '' Aequoera vic ...
and mCardinal. Visible
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
is not always usable
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
and
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
s should always be compared to other useful
genetically encodedfluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
s.
Intravenous injection
Intravenous therapy (abbreviated as IV therapy) is a medical technique that administers fluids, medications and nutrients directly into a person's vein. The intravenous route of administration is commonly used for rehydration or to provide nutrie ...
of exogenous
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
o
biliverdin dimethyl esterdoes not increase
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
of smURFP expressed in
tumors
A neoplasm () is a type of abnormal and excessive growth of tissue. The process that occurs to form or produce a neoplasm is called neoplasia. The growth of a neoplasm is uncoordinated with that of the normal surrounding tissue, and persists ...
after 1 to 24 hours.
Mass spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...
showed that the
ester groups were rapidly removed fro
biliverdin dimethyl ester Addition of 25 μM
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
o
biliverdin dimethyl esterdramatically increased
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
of
excised tumors
A neoplasm () is a type of abnormal and excessive growth of tissue. The process that occurs to form or produce a neoplasm is called neoplasia. The growth of a neoplasm is uncoordinated with that of the normal surrounding tissue, and persists ...
and smURFP is present without
chromophore
A chromophore is the part of a molecule responsible for its color.
The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molec ...
. Further research is necessary to optimize
chromophore
A chromophore is the part of a molecule responsible for its color.
The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molec ...
availability in mice to obtain
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
comparable or greater than
coral-derived red
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
s.
Adding chromophore to cells
Biliverdin dimethyl esterbiliverdin an
phycocyanobilinare commercially available fro
Frontier ScientificBiliverdin dimethyl ester biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
, or
phycocyanobilin
Phycocyanobilin is a blue phycobilin, i.e., a tetrapyrrole chromophore found in cyanobacteria and in the chloroplasts of red algae, glaucophytes, and some cryptomonads. Phycocyanobilin is present only in the phycobiliproteins allophycocyanin and ...
is dissolved in
DMSO
Dimethyl sulfoxide (DMSO) is an organosulfur compound with the formula ( CH3)2. This colorless liquid is the sulfoxide most widely used commercially. It is an important polar aprotic solvent that dissolves both polar and nonpolar compounds an ...
at a
concentration of 5 mM. The solution is very dark and pipette vigorously to ensure all is dissolved.
Biliverdin dimethyl esteris not soluble in common
buffers, including
phosphate buffered saline
Phosphate-buffered saline (PBS) is a buffer solution (pH ~ 7.4) commonly used in biological research. It is a water-based salt solution containing disodium hydrogen phosphate, sodium chloride and, in some formulations, potassium chloride and pot ...
(PBS) or
Hank's balanced salt solution (HBSS). Add 1-5 μ
biliverdin dimethyl esterin media or buffer containing 10%
fetal bovine serum
Fetal bovine serum (FBS) is derived from the blood drawn from a bovine fetus via a closed system of collection at the slaughterhouse. Fetal bovine serum is the most widely used serum-supplement for the in vitro cell culture of eukaryotic cells. T ...
(FBS). Add 25 μM
biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
(not as membrane permeant) to
cells
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
.
Biliverdin
Biliverdin (latin for green bile) is a green tetrapyrrolic bile pigment, and is a product of heme catabolism.Boron W, Boulpaep E. Medical Physiology: a cellular and molecular approach, 2005. 984-986. Elsevier Saunders, United States. It is the pi ...
does not saturate the smURFP sites and does not achieve maximum fluorescence intensity.
Biliverdin dimethyl estershould be used to get maximum fluorescence intensity. Incubate smURFP with
chromophore
A chromophore is the part of a molecule responsible for its color.
The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molec ...
for as long as possible to increase protein accumulation caused by enhanced
protein stability with
chromophore
A chromophore is the part of a molecule responsible for its color.
The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molec ...
. Leave
chromophore
A chromophore is the part of a molecule responsible for its color.
The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molec ...
for a minimum of 3 hours and 24 h is recommended. Remove
chromophore
A chromophore is the part of a molecule responsible for its color.
The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molec ...
, wash with media containing 10%
FBS, and image in media lacking
phenol red
Phenol red (also known as phenolsulfonphthalein or PSP) is a pH indicator frequently used in cell biology laboratories.
Chemical structure and properties
Phenol red exists as a red crystal that is stable in air. Its solubility is 0.77 grams per ...
or imaging
buffer
Buffer may refer to:
Science
* Buffer gas, an inert or nonflammable gas
* Buffer solution, a solution used to prevent changes in pH
* Buffering agent, the weak acid or base in a buffer solution
* Lysis buffer, in cell biology
* Metal ion buffer ...
.
smURFP genetically encoded biosensors
''
Kinase
In biochemistry, a kinase () is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule dona ...
FRET
A fret is any of the thin strips of material, usually metal wire, inserted laterally at specific positions along the neck or fretboard of a stringed instrument. Frets usually extend across the full width of the neck. On some historical instrum ...
sensor.'' smURFP is a useful acceptor for many red
fluorescent proteins due to spectral overlap. A rationally designed red fluorescent protein, stagRFP, allows for easier creation of
FRET
A fret is any of the thin strips of material, usually metal wire, inserted laterally at specific positions along the neck or fretboard of a stringed instrument. Frets usually extend across the full width of the neck. On some historical instrum ...
sensors. stagRFP is a useful FRET donor to the far-red acceptor smURFP and an
ERK kinase
In biochemistry, a kinase () is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule dona ...
FRET
A fret is any of the thin strips of material, usually metal wire, inserted laterally at specific positions along the neck or fretboard of a stringed instrument. Frets usually extend across the full width of the neck. On some historical instrum ...
reporter was created with an average response of ~15%. The new sensor allowed for simultaneous visualization of three kinases,
Src,
Akt
Protein kinase B (PKB), also known as Akt, is the collective name of a set of three serine/threonine-specific protein kinases that play key roles in multiple cellular processes such as glucose metabolism, apoptosis, cell proliferation, transc ...
,
ERK, in a single
cell
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
.
''Fluorescently imaging the
cell cycle
The cell cycle, or cell-division cycle, is the series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA (DNA replication) and some of its organelles, and subs ...
.'' Pioneering work by Atsushi Miyawaki and coworkers developed the fluorescent ubiquitination-based cell cycle indicator
FUCCI, which enables
fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
imaging of the cell cycle. Originally, a
green fluorescent protein
The green fluorescent protein (GFP) is a protein that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish '' Aequor ...
, mAG, was fused to hGem(1/110) and an orange
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
(mKO
2) was fused to hCdt1(30/120). Note, these fusions are fragments that contain a
nuclear localization signal A nuclear localization signal ''or'' sequence (NLS) is an amino acid sequence that 'tags' a protein for import into the cell nucleus by nuclear transport. Typically, this signal consists of one or more short sequences of positively charged lysines o ...
and
ubiquitination
Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Fo ...
sites for
degradation
Degradation may refer to:
Science
* Degradation (geology), lowering of a fluvial surface by erosion
* Degradation (telecommunications), of an electronic signal
* Biodegradation of organic substances by living organisms
* Environmental degradation ...
, but are not functional proteins. The
green fluorescent protein
The green fluorescent protein (GFP) is a protein that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish '' Aequor ...
is made during the S, G
2, or M phase and degraded during the G
0 or G
1 phase, while the orange
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
is made during the G
0 or G
1 phase and destroyed during the S, G
2, or M phase.
A far-red and near-infrared FUCCI was developed using a
cyanobacteria-derived
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
(smURFP) and a
bacteriophytochrome-derived
fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein (YFP)
* Red fluorescent protein
Red fluorescent protein (RFP) is a fluorophore that fluoresces red-orange when excited. Several variants have been dev ...
movie found at this link.
References
{{reflist
External links
* SmURF
KX449134& TDsmURFP
KX449135- GenBank/EMBL/DDBJ Accession Codes
FPbase entryObtain Plasmid DNA at Addgene(Non-profit organization for sharing DNA.)
Proteins
Fluorescent proteins