Sleeping Beauty transposon system
Encyclopedia
The Sleeping Beauty transposon system is a synthetic DNA transposon
that was constructed to introduce precisely defined DNA sequences into the chromosomes of vertebrate animals for the purposes of introducing new traits and to discover new genes
and their functions.
and a transposon
that was designed in 1997 to insert specific sequences of DNA
into genomes of vertebrate animals. DNA transposons translocate from one DNA site to another in a simple, cut-and-paste manner (Fig. 1). Transposition is a precise process in which a defined DNA segment is excised from one DNA molecule and moved to another site in the same or different DNA molecule or genome
.
As do all other Tc1/mariner-type transposases, SB transposase inserts a transposon into a TA dinucleotide base pair
in a recipient DNA sequence. The insertion site can be elsewhere in the same DNA molecule, or in another DNA molecule (or chromosome). In mammalian genomes, including humans, there are approximately 200 million TA sites. The TA insertion site is duplicated in the process of transposon integration. This duplication of the TA sequence is a hallmark of transposition and used to ascertain the mechanism in some experiments. The transposase can be encoded either within the transposon (e.g., the putative transposon shown in Fig. 2) or the transposase can be supplied by another source, in which case the transposon becomes a non-autonomous element. Non-autonomous transposons (e.g., Fig. 1) are most useful as genetic tools because after insertion they cannot independently continue to excise and re-insert. All of the DNA transposons identified in the human genome and other mammalian genomes are non-autonomous because even though they contain transposase genes, the genes are non-functional and unable to generate a transposase that can mobilize the transposon.
, the transposase genes found in fish have been inactive for more than 10 million years due to accumulated mutations. The reconstruction of SB transposase was based on the concept that there was a primordial Tc1-like transposon that was the ancestor to the sequences found in fish genomes. Although there were many sequences that looked like Tc-1 transposons in all the fish genomes studied, the transposon sequences were all inactive due to mutations. By assuming that the variations in sequences were due to independent mutations that accumulated in the different transposons, a putative ancestral transposon (Fig. 2) was predicted.
The construction for the transposase began by fusing portions of two inactive transposon sequences from Atlantic salmon
(Salmo salar) and one inactive transposon sequence from rainbow trout
(Oncorhynchus mykiss) and then repairing small deficits in the functional domains of the transposase enzyme
(Fig. 3). Each amino acid
in the first completed transposase, called SB10, was determined by a “majority-rule consensus sequence” based on 12 partial genes found in eight fish species. The first steps (1->3 in Fig. 3) were to restore a complete protein by filling in gaps in the sequence and reversing termination codons that would keep the putative 360-amino acid polypeptide from being synthesized. The next step (4 in Fig. 3) was to reverse mutations in the nuclear localization signal
(NLS) that is required to import the transposase enzyme from the cytoplasm
where it is made to the nucleus
where it acts. The amino-terminus of the transposase, which contains the DNA-binding motifs for recognition of the direct repeats (DRs), was restored in steps 5->8. The last two steps restored the catalytic domain, which features conserved aspartic acid
(D) and glutamic acid
(E) amino acids with specific spacing that are found in integrases and recombinases
. The end result was SB10, which contains all of the motifs required for function.
SB10 transposase has been improved over the decade since its construction by increasing the consensus with a greater number of extinct transposon sequences and testing various combinations of changes. Further work has shown that the DNA-binding domain consists of two paired sequences, which are homologous to sequence motifs found in certain transcription factors. The paired subdomains in SB transposase were designated PAI and RED. The PAI subdomain plays a dominant role in recognition of the DR sequences in the transposon. The RED subdomain overlaps with the nuclear localization signal, but its function is remains unclear. The most recent version of SB transposase, SB100X, has about 100 times the activity of SB10 as determined by transposition assays of antibiotic-resistance genes conducted in tissue cultured human HeLa cells. The International Society for Molecular and Cell Biology and Biotechnology Protocols and Research (ISMCBBPR) named SB100X the molecule of the year for 2009 for recognition of the potential it has in future genome engineering.
The transposon recognized by SB transposase was named T because it was isolated from the genome of another salmond fish, Tanichthys albonubes. The transposon consists of a genetic sequence of interest that is flanked by inverted repeats (IRs) that themselves contain short direct repeats (DR) (tandem arrowheads IR-DR in Figs. 1 and 2). T had the closest IR/DR sequence to the consensus sequence for the extinct Tc-1 like transposons in fish. The consensus transposon has IRs of 231 base pairs. The innermost DRs are 29 base pairs long whereas the outermost DRs are 31 base pairs long. The difference in length is critical for maximal transposition rates. The original T transposon component of the SB transposon system has been improved with minor changes to conform to the consensus of many related extinct and active transposons.
. The genetic cargo can be an expression cassette
- a transgene
and associated elements that confer transcriptional regulation
for expression at a desired level in specific tissue(s). An alternative use of SB transposons is to discover functions of genes, especially those that cause cancer
, by delivering DNA sequences that maximally disrupt expression of genes close to the insertion site. This process is referred to as insertional mutagenesis
or transposon mutagenesis
. When a gene is inactivated by insertion of a transposon (or other mechanism), that gene is “knocked out”. Knockout mice and knockout rats have been made with the SB system. Figure 4 illustrates these two uses of SB transposons.
For either gene delivery or gene disruption, SB transposons combine the advantages of viruses and naked DNA. Viruses have been evolutionarily selected based on their abilities to infect and replicate in new host cells. Simultaneously, cells have evolved major molecular defense mechanisms to protect themselves against viral infections. For some applications of genome engineering such as some forms of gene therapy, avoiding the use of viruses is also important for social and/or regulatory reasons. The use of non-viral vectors avoids many, but not all, of the defenses that cells employ against vectors.
Plasmids, the circular DNAs shown in Fig. 1, are generally used for non-viral gene delivery. However, there are two major problems with most methods for delivering DNA to cellular chromosomes using plasmids, the most common form of non-viral gene delivery. First, expression of transgenes from plasmids is brief due to lack of integration and due to cellular responses that turn off expression. Second, uptake of plasmid molecules into cells is difficult and inefficient. The Sleeping Beauty Transposon System was engineered to overcome the first problem. DNA transposons precisely insert defined DNA sequences (Fig. 1) almost randomly into host genomes thereby increasing the longevity of gene expression (even through multiple generations). Moreover, transposition avoids the formation of multiple, tandem integrations, which often results in switching off expression of the transgene. Currently, insertion of transgenes into chromosomes using plasmids is much less efficient than using viruses. However, by using powerful promoters to regulate expression of a transgene, delivery of transposons to a few cells can provide useful levels of secreted gene products for an entire animal.
Arguably the most exciting potential application of Sleeping Beauty transposons will be for human gene therapy. The widespread human application of gene therapy in first-world nations as well as countries with developing economies can be envisioned if the costs of the vector system are affordable. Because the SB system is comprised solely of DNA, the costs of production and delivery are considerably reduced compared to viral vectors. The first clinical trials using SB transposons in genetically modified T cells will test the efficacy of this form of gene therapy in patients at risk of death from advanced malignancies.
Transposon
Transposable elements are sequences of DNA that can move or transpose themselves to new positions within the genome of a single cell. The mechanism of transposition can be either "copy and paste" or "cut and paste". Transposition can create phenotypically significant mutations and alter the cell's...
that was constructed to introduce precisely defined DNA sequences into the chromosomes of vertebrate animals for the purposes of introducing new traits and to discover new genes
Gênes
Gênes is the name of a département of the First French Empire in present Italy, named after the city of Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa. Its capital was Genoa, and it was divided in the arrondissements of Genoa, Bobbio, Novi Ligure, Tortona and...
and their functions.
Mechanism of Action
The Sleeping Beauty transposon system is composed of a Sleeping Beauty (SB) transposaseTransposase
Transposase is an enzyme that binds to the ends of a transposon and catalyzes the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism....
and a transposon
Transposon
Transposable elements are sequences of DNA that can move or transpose themselves to new positions within the genome of a single cell. The mechanism of transposition can be either "copy and paste" or "cut and paste". Transposition can create phenotypically significant mutations and alter the cell's...
that was designed in 1997 to insert specific sequences of 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...
into genomes of vertebrate animals. DNA transposons translocate from one DNA site to another in a simple, cut-and-paste manner (Fig. 1). Transposition is a precise process in which a defined DNA segment is excised from one DNA molecule and moved to another site in the same or different DNA molecule or genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
.
As do all other Tc1/mariner-type transposases, SB transposase inserts a transposon into a TA dinucleotide base pair
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
in a recipient DNA sequence. The insertion site can be elsewhere in the same DNA molecule, or in another DNA molecule (or chromosome). In mammalian genomes, including humans, there are approximately 200 million TA sites. The TA insertion site is duplicated in the process of transposon integration. This duplication of the TA sequence is a hallmark of transposition and used to ascertain the mechanism in some experiments. The transposase can be encoded either within the transposon (e.g., the putative transposon shown in Fig. 2) or the transposase can be supplied by another source, in which case the transposon becomes a non-autonomous element. Non-autonomous transposons (e.g., Fig. 1) are most useful as genetic tools because after insertion they cannot independently continue to excise and re-insert. All of the DNA transposons identified in the human genome and other mammalian genomes are non-autonomous because even though they contain transposase genes, the genes are non-functional and unable to generate a transposase that can mobilize the transposon.
Construction
This resurrected transposase gene was named "Sleeping Beauty (SB)" because it was brought back to activity from a long evolutionary sleep. The SB transposon system is synthetic in that the SB transposase was re-constructed from extinct (fossil) transposase sequences belonging to the Tc1/mariner class of transposons found in the genomes of salmonid fish. As in humans, where about 20,000 inactivated Tc1/mariner-type transposons comprise almost 3% of the human genomeHuman genome
The human genome is the genome of Homo sapiens, which is stored on 23 chromosome pairs plus the small mitochondrial DNA. 22 of the 23 chromosomes are autosomal chromosome pairs, while the remaining pair is sex-determining...
, the transposase genes found in fish have been inactive for more than 10 million years due to accumulated mutations. The reconstruction of SB transposase was based on the concept that there was a primordial Tc1-like transposon that was the ancestor to the sequences found in fish genomes. Although there were many sequences that looked like Tc-1 transposons in all the fish genomes studied, the transposon sequences were all inactive due to mutations. By assuming that the variations in sequences were due to independent mutations that accumulated in the different transposons, a putative ancestral transposon (Fig. 2) was predicted.
The construction for the transposase began by fusing portions of two inactive transposon sequences from Atlantic salmon
Atlantic salmon
The Atlantic salmon is a species of fish in the family Salmonidae, which is found in the northern Atlantic Ocean and in rivers that flow into the north Atlantic and the north Pacific....
(Salmo salar) and one inactive transposon sequence from rainbow trout
Rainbow trout
The rainbow trout is a species of salmonid native to tributaries of the Pacific Ocean in Asia and North America. The steelhead is a sea run rainbow trout usually returning to freshwater to spawn after 2 to 3 years at sea. In other words, rainbow trout and steelhead trout are the same species....
(Oncorhynchus mykiss) and then repairing small deficits in the functional domains of the transposase enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
(Fig. 3). Each amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
in the first completed transposase, called SB10, was determined by a “majority-rule consensus sequence” based on 12 partial genes found in eight fish species. The first steps (1->3 in Fig. 3) were to restore a complete protein by filling in gaps in the sequence and reversing termination codons that would keep the putative 360-amino acid polypeptide from being synthesized. The next step (4 in Fig. 3) was to reverse mutations in the nuclear localization signal
Nuclear localization signal
A nuclear localization signal or sequence is an amino acid sequence which '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 or arginines exposed on the protein surface. Different...
(NLS) that is required to import the transposase enzyme from the cytoplasm
Cytoplasm
The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...
where it is made to the nucleus
Cell nucleus
In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...
where it acts. The amino-terminus of the transposase, which contains the DNA-binding motifs for recognition of the direct repeats (DRs), was restored in steps 5->8. The last two steps restored the catalytic domain, which features conserved aspartic acid
Aspartic acid
Aspartic acid is an α-amino acid with the chemical formula HOOCCHCH2COOH. The carboxylate anion, salt, or ester of aspartic acid is known as aspartate. The L-isomer of aspartate is one of the 20 proteinogenic amino acids, i.e., the building blocks of proteins...
(D) and glutamic acid
Glutamic acid
Glutamic acid is one of the 20 proteinogenic amino acids, and its codons are GAA and GAG. It is a non-essential amino acid. The carboxylate anions and salts of glutamic acid are known as glutamates...
(E) amino acids with specific spacing that are found in integrases and recombinases
Recombinases
Recombinases are genetic recombination enzymes.Types include:* Cre recombinase* Hin recombinase* RecA/RAD51* Tre recombinase* FLP recombinase...
. The end result was SB10, which contains all of the motifs required for function.
SB10 transposase has been improved over the decade since its construction by increasing the consensus with a greater number of extinct transposon sequences and testing various combinations of changes. Further work has shown that the DNA-binding domain consists of two paired sequences, which are homologous to sequence motifs found in certain transcription factors. The paired subdomains in SB transposase were designated PAI and RED. The PAI subdomain plays a dominant role in recognition of the DR sequences in the transposon. The RED subdomain overlaps with the nuclear localization signal, but its function is remains unclear. The most recent version of SB transposase, SB100X, has about 100 times the activity of SB10 as determined by transposition assays of antibiotic-resistance genes conducted in tissue cultured human HeLa cells. The International Society for Molecular and Cell Biology and Biotechnology Protocols and Research (ISMCBBPR) named SB100X the molecule of the year for 2009 for recognition of the potential it has in future genome engineering.
The transposon recognized by SB transposase was named T because it was isolated from the genome of another salmond fish, Tanichthys albonubes. The transposon consists of a genetic sequence of interest that is flanked by inverted repeats (IRs) that themselves contain short direct repeats (DR) (tandem arrowheads IR-DR in Figs. 1 and 2). T had the closest IR/DR sequence to the consensus sequence for the extinct Tc-1 like transposons in fish. The consensus transposon has IRs of 231 base pairs. The innermost DRs are 29 base pairs long whereas the outermost DRs are 31 base pairs long. The difference in length is critical for maximal transposition rates. The original T transposon component of the SB transposon system has been improved with minor changes to conform to the consensus of many related extinct and active transposons.
Applications
Over the past decade, SB transposons have been developed as non-viral vectors for introduction of genes into genomes of vertebrate animals and for gene therapyGene therapy
Gene therapy is the insertion, alteration, or removal of genes within an individual's cells and biological tissues to treat disease. It is a technique for correcting defective genes that are responsible for disease development...
. The genetic cargo can be an expression cassette
Expression cassette
An expression cassette is made up of one or more genes and the sequences controlling their expression. Three components comprise an expression cassette: a promoter sequence, an open reading frame, and a 3' untranslated region that, in eukaryotes, usually contains a polyadenylation site. The...
- a transgene
Transgene
A transgene is a gene or genetic material that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another....
and associated elements that confer transcriptional regulation
Transcriptional regulation
Transcriptional regulation is the change in gene expression levels by altering transcription rates. -Regulation of transcription:Regulation of transcription controls when transcription occurs and how much RNA is created...
for expression at a desired level in specific tissue(s). An alternative use of SB transposons is to discover functions of genes, especially those that cause cancer
Cancer
Cancer , known medically as a malignant neoplasm, is a large group of different diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the...
, by delivering DNA sequences that maximally disrupt expression of genes close to the insertion site. This process is referred to as insertional mutagenesis
Insertional mutagenesis
Insertional mutagenesis is mutagenesis of DNA by the insertion of one or more bases.Insertional mutations can occur naturally, mediated by virus or transposon, or can be artificially created for research purposes in the lab.- Signature tagged mutagenesis :...
or transposon mutagenesis
Transposon Mutagenesis
Transposon mutagenesis, or transposition mutagenesis, is a biological process that allows genes to be transferred to a host organism's chromosome, interrupting or modifying the function of an extant gene on the chromosome and causing mutation.-History:...
. When a gene is inactivated by insertion of a transposon (or other mechanism), that gene is “knocked out”. Knockout mice and knockout rats have been made with the SB system. Figure 4 illustrates these two uses of SB transposons.
For either gene delivery or gene disruption, SB transposons combine the advantages of viruses and naked DNA. Viruses have been evolutionarily selected based on their abilities to infect and replicate in new host cells. Simultaneously, cells have evolved major molecular defense mechanisms to protect themselves against viral infections. For some applications of genome engineering such as some forms of gene therapy, avoiding the use of viruses is also important for social and/or regulatory reasons. The use of non-viral vectors avoids many, but not all, of the defenses that cells employ against vectors.
Plasmids, the circular DNAs shown in Fig. 1, are generally used for non-viral gene delivery. However, there are two major problems with most methods for delivering DNA to cellular chromosomes using plasmids, the most common form of non-viral gene delivery. First, expression of transgenes from plasmids is brief due to lack of integration and due to cellular responses that turn off expression. Second, uptake of plasmid molecules into cells is difficult and inefficient. The Sleeping Beauty Transposon System was engineered to overcome the first problem. DNA transposons precisely insert defined DNA sequences (Fig. 1) almost randomly into host genomes thereby increasing the longevity of gene expression (even through multiple generations). Moreover, transposition avoids the formation of multiple, tandem integrations, which often results in switching off expression of the transgene. Currently, insertion of transgenes into chromosomes using plasmids is much less efficient than using viruses. However, by using powerful promoters to regulate expression of a transgene, delivery of transposons to a few cells can provide useful levels of secreted gene products for an entire animal.
Arguably the most exciting potential application of Sleeping Beauty transposons will be for human gene therapy. The widespread human application of gene therapy in first-world nations as well as countries with developing economies can be envisioned if the costs of the vector system are affordable. Because the SB system is comprised solely of DNA, the costs of production and delivery are considerably reduced compared to viral vectors. The first clinical trials using SB transposons in genetically modified T cells will test the efficacy of this form of gene therapy in patients at risk of death from advanced malignancies.