Dps (DNA-binding proteins from starved cells)
Encyclopedia
Dps proteins belong to the ferritin
superfamily and are characterized by strong similarities but also distinctive differences with respect to “canonical” ferritin
s.
Dps proteins are part of a complex bacterial defence system that protects DNA
against oxidative damage and are distributed widely in the bacterial kingdom.
superfamily and the DNA
protection is afforded by means of a double mechanism:
1) The first was discovered in Escherichia coli
Dps in 1992 and has given the name to the protein
family; during stationary phase, Dps binds the chromosome
non-specifically, forming a highly ordered and stable dps-DNA
co-crystal within which chromosomal DNA
is condensed and protected from diverse damages. The lysine-rich N-terminus is required for self-aggregation as well as for Dps-driven DNA condensation
.
2) The second mode of protection is due to the ability of Dps proteins to bind and oxidize Fe(II) at the characteristic, highly conserved intersubunit ferroxidase center.
The dinuclear ferroxidase centers are located at the interfaces between subunits related by 2-fold symmetry axes. Fe(II) is sequestered and stored in the form of Fe(III) oxyhydroxide mineral, which can be released after reduction. In the mineral iron core up to 500 Fe(III) can be deposited. One hydrogen peroxide oxidizes two Fe2+ ions, which prevents hydroxyl radical production by the Fenton reaction (reaction I):
2 Fe2+ + H2O2 + 2 H+ = 2 Fe3+ + 2 H2O
Dps also protects the cell from UV
and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.
Dps protein is Induced by rpoS and IHF in the early stationary phase. Dps is also Induced by oxyR in response to oxidative stress during exponential phase. ClpXP probably directly regulate proteolysis of dps during exponential phase. ClpAP seems to play an indirect role in maintaining ongoing dps synthesis during stationary phase
proteins have been successfully used as the reaction chamber for the fabrication of metal nanoparticles (NPs). Protein shells served as a template to restrain particle growth and as a coating to prevent coagulation/aggregation between NPs. Using various sizes of protein shells, various sizes of NPs can be easily synthesized for chemical, physical and bio-medical applications.
Ferritin
Ferritin is a ubiquitous intracellular protein that stores iron and releases it in a controlled fashion. The amount of ferritin stored reflects the amount of iron stored. The protein is produced by almost all living organisms, including bacteria, algae and higher plants, and animals...
superfamily and are characterized by strong similarities but also distinctive differences with respect to “canonical” ferritin
Ferritin
Ferritin is a ubiquitous intracellular protein that stores iron and releases it in a controlled fashion. The amount of ferritin stored reflects the amount of iron stored. The protein is produced by almost all living organisms, including bacteria, algae and higher plants, and animals...
s.
Dps proteins are part of a complex bacterial defence system that protects DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
against oxidative damage and are distributed widely in the bacterial kingdom.
Description
DPS are highly symmetrical dodecameric proteins of 200 kDa characterized from a shell-like structure of 2:3 tetrahedral symmetry assembled from identical subunits with an external diameter of ~ 9 nm and a central cavity of ~ 4.5 nm in diameter. Dps proteins belong to the ferritinFerritin
Ferritin is a ubiquitous intracellular protein that stores iron and releases it in a controlled fashion. The amount of ferritin stored reflects the amount of iron stored. The protein is produced by almost all living organisms, including bacteria, algae and higher plants, and animals...
superfamily and the DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
protection is afforded by means of a double mechanism:
1) The first was discovered in Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
Dps in 1992 and has given the name to the protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
family; during stationary phase, Dps binds the chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
non-specifically, forming a highly ordered and stable dps-DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
co-crystal within which chromosomal DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
is condensed and protected from diverse damages. The lysine-rich N-terminus is required for self-aggregation as well as for Dps-driven DNA condensation
DNA condensation
DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems. Condensed DNA often has surprising properties, which one would not predict from classical...
.
2) The second mode of protection is due to the ability of Dps proteins to bind and oxidize Fe(II) at the characteristic, highly conserved intersubunit ferroxidase center.
The dinuclear ferroxidase centers are located at the interfaces between subunits related by 2-fold symmetry axes. Fe(II) is sequestered and stored in the form of Fe(III) oxyhydroxide mineral, which can be released after reduction. In the mineral iron core up to 500 Fe(III) can be deposited. One hydrogen peroxide oxidizes two Fe2+ ions, which prevents hydroxyl radical production by the Fenton reaction (reaction I):
2 Fe2+ + H2O2 + 2 H+ = 2 Fe3+ + 2 H2O
Dps also protects the cell from UV
Ultraviolet
Ultraviolet light is electromagnetic radiation with a wavelength shorter than that of visible light, but longer than X-rays, in the range 10 nm to 400 nm, and energies from 3 eV to 124 eV...
and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.
Expression
In Escherichia coliEscherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
Dps protein is Induced by rpoS and IHF in the early stationary phase. Dps is also Induced by oxyR in response to oxidative stress during exponential phase. ClpXP probably directly regulate proteolysis of dps during exponential phase. ClpAP seems to play an indirect role in maintaining ongoing dps synthesis during stationary phase
Applications
Cavities formed by Dps and ferritinFerritin
Ferritin is a ubiquitous intracellular protein that stores iron and releases it in a controlled fashion. The amount of ferritin stored reflects the amount of iron stored. The protein is produced by almost all living organisms, including bacteria, algae and higher plants, and animals...
proteins have been successfully used as the reaction chamber for the fabrication of metal nanoparticles (NPs). Protein shells served as a template to restrain particle growth and as a coating to prevent coagulation/aggregation between NPs. Using various sizes of protein shells, various sizes of NPs can be easily synthesized for chemical, physical and bio-medical applications.