Transposon Resolvases
Holliday Junction Resolvases
DNA, Cruciform
Transposases
DNA Transposable Elements
Endodeoxyribonucleases
Mutagenesis, Insertional
Recombination, Genetic
Molecular Sequence Data
Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity. (1/42)
Tn3 resolvase promotes site-specific recombination between two res sites, each of which has three resolvase dimer-binding sites. Catalysis of DNA-strand cleavage and rejoining occurs at binding site I, but binding sites II and III are required for recombination. We used an in vivo screen to detect resolvase mutants that were active on res sites with binding sites II and III deleted (that is, only site I remaining). Mutations of amino acids Asp102 (D102) or Met103 (M103) were sufficient to permit catalysis of recombination between site I and a full res, but not between two copies of site I. A double mutant resolvase, with a D102Y mutation and an additional activating mutation at Glu124 (E124Q), recombined substrates containing only two copies of site I, in vivo and in vitro. In these novel site Ixsite I reactions, product topology is no longer restricted to the normal simple catenane, indicating synapsis by random collision. Furthermore, the mutants have lost the normal specificity for directly repeated sites and supercoiled substrates; that is, they promote recombination between pairs of res sites in linear molecules, or in inverted repeat in a supercoiled molecule, or in separate molecules. (+info)Multiple roles for TnpI recombinase in regulation of Tn5401 transposition in Bacillus thuringiensis. (2/42)
Tn5401 is a class II transposable element derived from the gram-positive bacterium Bacillus thuringiensis. The 4,837-bp transposon encodes a Tn3-like transposase (TnpA) and an integrase-like recombinase (TnpI) and is notable for its unusually long 53-bp terminal inverted repeats (TIRs). The tnpA and tnpI genes are transcribed from a common promoter, designated P(R), that is subject to negative regulation by TnpI. The TIRs of Tn5401 each contain a 38-bp sequence that can be aligned with the 38- to 40-bp TIR sequences of Tn3-like transposons and an adjacent 12-bp sequence that binds TnpI. This unique juxtaposition of TnpA and TnpI binding sites suggests that TnpI may regulate the binding or catalytic activity of TnpA. The results of the present study indicate that TnpI, in addition to functioning as a site-specific recombinase and as a transcriptional repressor, is required for TnpA binding to the TIRs of Tn5401. (+info)Stability by multimer resolution of pJHCMW1 is due to the Tn1331 resolvase and not to the Escherichia coli Xer system. (3/42)
The plasmid pJHCMW1 encodes resistance to several aminoglycosides and beta-lactams and consists of a copy of the transposon Tn1331, a region including the replication functions, and a sequence with homology to ColE1 cer, designated mwr. In this work, the role of this cer-like site in ensuring the stable inheritance of pJHCMW1 by multimer resolution was studied. The Escherichia coli Xer site-specific recombination system acts at sites such as ColE1 cer to resolve plasmid multimers formed by homologous recombination, thereby maintaining plasmids in a monomeric state and helping to ensure stable plasmid inheritance. Despite its high similarity to ColE1 cer, the pJHCMW1 mwr was a poor substrate for Xer recombination in E. coli and did not contribute significantly to plasmid stability. Instead, the Tn1331 co-integrate resolution system was highly active at resolving pJHCMW1 multimers and ensured the stable inheritance of pJHCMW1. Although Xer recombination at pJHCMW1 mwr was inefficient in E. coli, the recombination that did occur was dependent on ArgR, PepA, XerC and XerD. A supercoiled circular DNA molecule containing two pJHCMW1 mwr sites in direct repeat yielded Holliday-junction-containing product when incubated with ArgR, PepA, XerC and XerD in vitro, confirming that pJHCMW1 mwr is a functional recombination site. However, unlike cer, some Holliday-junction-containing product could be detected for mwr in the absence of ArgR, although addition of this protein resulted in formation of more Holliday junctions. Binding experiments demonstrated that XerD bound to pJHCMW1 mwr core with a high affinity, but that XerC bound to this site very poorly, even in the presence of XerD. (+info)Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori. (4/42)
A search by subtractive hybridization for sequences present in only certain strains of Helicobacter pylori led to the discovery of a 2-kb transposable element to be called IS607, which further PCR and hybridization tests indicated was present in about one-fifth of H. pylori strains worldwide. IS607 contained two open reading frames (ORFs) of possibly different phylogenetic origin. One ORF (orfB) exhibited protein-level homology to one of two putative transposase genes found in several other chimeric elements including IS605 (also of H. pylori) and IS1535 (of Mycobacterium tuberculosis). The second IS607 gene (orfA) was unrelated to the second gene of IS605 and might possibly be chimeric itself: it exhibited protein-level homology to merR bacterial regulatory genes in the first approximately 50 codons and homology to the second gene of IS1535 (annotated as "resolvase," apparently due to a weak short recombinase motif) in the remaining three-fourths of its length. IS607 was found to transpose in Escherichia coli, and analyses of sequences of IS607-target DNA junctions in H. pylori and E. coli indicated that it inserted either next to or between adjacent GG nucleotides, and generated either a 2-bp or a 0-bp target sequence duplication, respectively. Mutational tests showed that its transposition in E. coli required orfA but not orfB, suggesting that OrfA protein may represent a new, previously unrecognized, family of bacterial transposases. (+info)The large resolvase TndX is required and sufficient for integration and excision of derivatives of the novel conjugative transposon Tn5397. (5/42)
Tn5397 is a novel conjugative transposon, originally isolated from Clostridium difficile. This element can transfer between C. difficile strains and to and from Bacillus subtilis. It encodes a conjugation system that is very similar to that of Tn916. However, insertion and excision of Tn5397 appears to be dependent on the product of the element encoded gene tndX, a member of the large resolvase family of site-specific recombinases. To test the role of tndX, the gene was cloned and the protein was expressed in Escherichia coli. The ability of TndX to catalyze the insertion and excision of derivatives (minitransposons) of Tn5397 representing the putative circular and integrated forms, respectively, was investigated. TndX was required for both insertion and excision. Mutagenesis studies showed that some of the highly conserved amino acids at the N-terminal resolvase domain and the C-terminal nonconserved region of TndX are essential for activity. Analysis of the target site choices showed that the cloned Tn5397 targets from C. difficile and B. subtilis were still hot spots for the minitransposon insertion in E. coli. (+info)Comparison of Tn5397 from Clostridium difficile, Tn916 from Enterococcus faecalis and the CW459tet(M) element from Clostridium perfringens shows that they have similar conjugation regions but different insertion and excision modules. (6/42)
Comparative analysis of the conjugative transposons Tn5397 from Clostridium difficile and Tn916 from Enterococcus faecalis, and the CW459tet(M) element from Clostridium perfringens, has revealed that these tetracycline-resistance elements are closely related. All three elements contain the tet(M) resistance gene and have sequence similarity throughout their central region. However, they have very different integration/excision modules. Instead of the int and xis genes that are found in Tn916, Tn5397 has a large resolvase gene, tndX. The C. perfringens element encodes the putative Int459 protein, which is a member of the integrase family of site-specific recombinases but is not closely related to Int from Tn916. Based on these studies it is concluded that the clostridial elements have a modular genetic organization and were derived independently from distinct mobile genetic elements. (+info)A model for the gamma delta resolvase synaptic complex. (7/42)
The serine recombinase gamma delta resolvase performs site-specific recombination in an elaborate synaptic complex containing 12 resolvase subunits and two 114-base pair res sites. Here we present an alternative structural model for the synaptic complex. Resolvase subunits in the complex contact their neighbors in equivalent ways, using three principal interactions, one of which is a newly proposed synaptic interaction. Evidence in support of this interaction is provided by mutations at the interface that either enable resolvase to synapse two copies of site I or inhibit synapsis of complete res sites. In our model, the two crossover sites are far apart, separated by the resolvase catalytic domains bound to them. Thus, recombination would require a substantial rearrangement of resolvase subunits or domains. (+info)Characterization of a class II defective transposon carrying two haloacetate dehalogenase genes from Delftia acidovorans plasmid pUO1. (8/42)
The two haloacetate dehalogenase genes, dehH1 and dehH2, on the 65-kb plasmid pUO1 from Delftia acidovorans strain B were found to be located on transposable elements. The dehH2 gene was carried on an 8.9-kb class I composite transposon (TnHad1) that was flanked by two directly repeated copies of IS1071, IS1071L and IS1071R. The dehH1 gene was also flanked by IS1071L and a truncated version of IS1071 (IS1071N). TnHad1, dehH1, and IS1071N were located on a 15.6-kb class II transposon (TnHad2) whose terminal inverted repeats and res site showed high homology with those of the Tn21-related transposons. TnHad2 was defective in transposition because of its lacking the transposase and resolvase genes. TnHad2 could transpose when the Tn21-encoded transposase and resolvase were supplied in trans. These results demonstrated that Tn Had2 is a defective Tn21-related transposon carrying another class I catabolic transposon. (+info)Transposon resolvases are enzymes that catalyze the precise excision of transposable elements, also known as transposons or jumping genes, from DNA molecules. Transposons are mobile genetic elements that can move and integrate into different locations within a genome. This movement can lead to genetic variation, but it can also cause mutations, genomic instability, and other deleterious effects.
Transposon resolvases function by cleaving specific sites within the transposable element, resulting in the formation of a circular DNA molecule called a transposon circle. The transposon circle can then be reintegrated into the genome at a new location, or it can be degraded by cellular enzymes.
Transposon resolvases are essential for the proper regulation and mobility of transposable elements in many organisms, including bacteria, yeast, and plants. Defects in transposon resolvase function can lead to genomic instability, developmental abnormalities, and other phenotypic consequences.
Holliday junction resolvases are a type of enzyme that are involved in the process of genetic recombination. They are named after Robin Holliday, who first proposed the existence of a structure called a Holliday junction during genetic recombination.
A Holliday junction is a four-way DNA structure that forms when two DNA molecules exchange genetic material during recombination. The junction is held together by hydrogen bonds between complementary base pairs, and it can move along the DNA molecules through a process called branch migration.
Holliday junction resolvases are responsible for cleaving the DNA strands at the Holliday junction, resolving the structure into two separate DNA molecules. They do this by introducing nicks in the phosphodiester backbone of the DNA strands on either side of the junction and then joining the broken ends together. This results in the exchange of genetic material between the two original DNA molecules.
There are several different types of Holliday junction resolvases, including the bacterial RuvC and RecU enzymes, as well as the eukaryotic Flap endonuclease 1 (FEN1) and XPF/ERCC1 complexes. These enzymes have different specificities for cleaving the DNA strands at the Holliday junction, but they all play important roles in ensuring that genetic recombination occurs accurately and efficiently.
"Cruciform DNA" is a term used to describe a specific conformation or structure that a double-stranded DNA molecule can adopt. It is so-called because the structure resembles the shape of a cross or crucifix.
This conformation arises when two inverted repeats of DNA sequence are located close to each other on the same DNA molecule, such that they can pair up and form a stable secondary structure. This results in the formation of a hairpin loop at each end of the inverted repeat sequences, with the loops pointing towards each other and the intervening sequences forming two arms that cross in the middle.
Cruciform structures are important in various biological processes, including DNA replication, repair, and recombination. However, they can also pose challenges to these processes, as the crossing of the DNA strands can create topological constraints that must be resolved before replication or transcription can proceed.
It's worth noting that cruciform structures are not stable in solution and are usually only observed under specific conditions, such as when the DNA is supercoiled or when negative supercoiling is introduced through the action of enzymes like topoisomerases.
Recombinases are enzymes that catalyze the process of recombination between two or more DNA molecules by breaking and rejoining their strands. They play a crucial role in various biological processes such as DNA repair, genetic recombination during meiosis, and site-specific genetic modifications.
Recombinases recognize and bind to specific DNA sequences, called recognition sites or crossover sites, where they cleave the phosphodiester bonds of the DNA backbone, forming a Holliday junction intermediate. The recombinase then catalyzes the exchange of strands between the two DNA molecules at the junction and subsequently ligates the broken ends to form new phosphodiester bonds, resulting in the recombination of the DNA molecules.
There are several types of recombinases, including serine recombinases, tyrosine recombinases, and lambda integrase. These enzymes differ in their recognition sites, catalytic mechanisms, and biological functions. Recombinases have important applications in molecular biology and genetic engineering, such as generating targeted DNA deletions or insertions, constructing genetic circuits, and developing gene therapy strategies.
Transposases are a type of enzyme that are involved in the process of transposition, which is the movement of a segment of DNA from one location within a genome to another. Transposases recognize and bind to specific sequences of DNA called inverted repeats that flank the mobile genetic element, or transposon, and catalyze the excision and integration of the transposon into a new location in the genome. This process can have significant consequences for the organization and regulation of genes within an organism's genome, and may contribute to genetic diversity and evolution.
DNA transposable elements, also known as transposons or jumping genes, are mobile genetic elements that can change their position within a genome. They are composed of DNA sequences that include genes encoding the enzymes required for their own movement (transposase) and regulatory elements. When activated, the transposase recognizes specific sequences at the ends of the element and catalyzes the excision and reintegration of the transposable element into a new location in the genome. This process can lead to genetic variation, as the insertion of a transposable element can disrupt the function of nearby genes or create new combinations of gene regulatory elements. Transposable elements are widespread in both prokaryotic and eukaryotic genomes and are thought to play a significant role in genome evolution.
Endodeoxyribonucleases are a type of enzyme that cleave, or cut, phosphodiester bonds within the backbone of DNA molecules. These enzymes are also known as restriction endonucleases or simply restriction enzymes. They are called "restriction" enzymes because they were first discovered in bacteria, where they function to protect the organism from foreign DNA by cleaving and destroying invading viral DNA.
Endodeoxyribonucleases recognize specific sequences of nucleotides within the DNA molecule, known as recognition sites or restriction sites, and cut the phosphodiester bonds at specific locations within these sites. The cuts made by endodeoxyribonucleases can be either "sticky" or "blunt," depending on whether the enzyme leaves single-stranded overhangs or creates blunt ends at the site of cleavage, respectively.
Endodeoxyribonucleases are widely used in molecular biology research for various applications, including DNA cloning, genome mapping, and genetic engineering. They allow researchers to cut DNA molecules at specific sites, creating defined fragments that can be manipulated and recombined in a variety of ways.
Insertional mutagenesis is a process of introducing new genetic material into an organism's genome at a specific location, which can result in a change or disruption of the function of the gene at that site. This technique is often used in molecular biology research to study gene function and regulation. The introduction of the foreign DNA is typically accomplished through the use of mobile genetic elements, such as transposons or viruses, which are capable of inserting themselves into the genome.
The insertion of the new genetic material can lead to a loss or gain of function in the affected gene, resulting in a mutation. This type of mutagenesis is called "insertional" because the mutation is caused by the insertion of foreign DNA into the genome. The effects of insertional mutagenesis can range from subtle changes in gene expression to the complete inactivation of a gene.
This technique has been widely used in genetic research, including the study of developmental biology, cancer, and genetic diseases. It is also used in the development of genetically modified organisms (GMOs) for agricultural and industrial applications.
Genetic recombination is the process by which genetic material is exchanged between two similar or identical molecules of DNA during meiosis, resulting in new combinations of genes on each chromosome. This exchange occurs during crossover, where segments of DNA are swapped between non-sister homologous chromatids, creating genetic diversity among the offspring. It is a crucial mechanism for generating genetic variability and facilitating evolutionary change within populations. Additionally, recombination also plays an essential role in DNA repair processes through mechanisms such as homologous recombinational repair (HRR) and non-homologous end joining (NHEJ).
Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.
A bacterial gene is a segment of DNA (or RNA in some viruses) that contains the genetic information necessary for the synthesis of a functional bacterial protein or RNA molecule. These genes are responsible for encoding various characteristics and functions of bacteria such as metabolism, reproduction, and resistance to antibiotics. They can be transmitted between bacteria through horizontal gene transfer mechanisms like conjugation, transformation, and transduction. Bacterial genes are often organized into operons, which are clusters of genes that are transcribed together as a single mRNA molecule.
It's important to note that the term "bacterial gene" is used to describe genetic elements found in bacteria, but not all genetic elements in bacteria are considered genes. For example, some DNA sequences may not encode functional products and are therefore not considered genes. Additionally, some bacterial genes may be plasmid-borne or phage-borne, rather than being located on the bacterial chromosome.
Insertion sequence
Simple transposon
Site-specific recombination
Aryldialkylphosphatase
List of MeSH codes (D08)
Site-specific recombinase technology
Tn3 transposon
Transposase
Jordan SL[au] - Search Results - PubMed
Insertion sequence - Wikipedia
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MeSH Browser
Composite transposons2
- In composite transposons, the additional genes are flanked by insertion sequences, which supply the transposase. (microbiologynotes.org)
- Structures of homologous composite transposons carrying cbaABC genes from Europe and North America. (sciepub.com)
Transposase5
- Most of the isolates (20 of 30) hybridized to probes encoding regions of the transposase (tnpA) and resolvase (tnpR) genes from Tn501 and Tn21. (lincoln.ac.uk)
- They are characterized by the presence of 35-48-bp terminal inverted repeats (IR), transposase (tnpA) and resolvase (tnpR) genes, a res-internal resolution site, and genes other than those required for transposition [14]. (dadospdf.com)
- Once integrated into the frog genome, the 'cut-and-paste' DNA transposons are targets for remobilization by re-expression of the appropriate transposase enzyme. (biomedcentral.com)
- The recombinase used by a specific mobile genetic element may be called an integrase , resolvase , or transposase . (microbiologynotes.org)
- The flanking IS elements encode the transposase used by the transposon to move. (microbiologynotes.org)
Genes6
- Insertion sequences have two major characteristics: they are small relative to other transposable elements (generally around 700 to 2500 bp in length) and only code for proteins implicated in the transposition activity (they are thus different from other transposons, which also carry accessory genes such as antibiotic resistance genes). (wikipedia.org)
- in a composite transposon, two insertion sequences flank one or more accessory genes, such as an antibiotic resistance gene (e.g. (wikipedia.org)
- 59:4024-4030, 1993) indicates the presence of hybrid transposons and provides evidence for extensive recombination, both between transposon genes and between transposon and mer genes, within these natural populations of bacteria. (lincoln.ac.uk)
- Tn5083 and Tn5084 are recombinants, and are comprised of fragments from several transposons including Tn5085, and a relative of a putative transposon from B. firmus (which contains similar genes to the cadmium resistance operon of Staphylococcus aureus), as well as others. (dadospdf.com)
- Some transposons bear transfer genes and can easily move between bacteria during the process of conjugation, They are called conjugative transposons or integrative conjugative elements (ICEs) . (microbiologynotes.org)
- Unit transposons contain additional genes (e.g., antibiotic-resistance genes) in addition to the recombinases that enable them to transpose. (microbiologynotes.org)
Protein1
- The resolvase protein from the transposon Tn21. (nih.gov)
Insertion sequences3
- Nevertheless, there exist another sort of transposons, called unit transposons, that do not carry insertion sequences at their extremities (e.g. (wikipedia.org)
- A complex transposon does not rely on flanking insertion sequences for resolvase. (wikipedia.org)
- Unit transposons are not associated with insertion sequences. (microbiologynotes.org)
Transposition1
- Other transposons lack IS elements and encode their own transposition enzymes. (microbiologynotes.org)
Inverted repeats1
- The resolvase is part of the tns genome and cuts at flanking inverted repeats. (wikipedia.org)
Genome2
- The high fecundity of the frog combined with the ability to remobilize transposon transgenes integrated into frog genome will allow large-scale insertional mutagenesis screens to be performed in laboratories with modest husbandry capacities. (biomedcentral.com)
- Transposons have widely been used in plant and invertebrate model species to integrate foreign DNA into the host genome. (biomedcentral.com)
Class4
- We have shown that the mer determinant can either be located at the chromosome, or on a plasmid in the Bacillus species, and is carried by class II mercury resistance transposons: Tn5084 from B. cereus RC607 and B. cereus VKM684 (ATCC10702) and Tn5085 from Exiguobacterium sp. (dadospdf.com)
- The majority of mercury resistance transposons that have been studied are class II. (dadospdf.com)
- 152 (2001) 503-514 been described: TnMERI1 from Bacillus megaterium MB1, which is a class II transposon [20, 21]. (dadospdf.com)
- Analysis of the genetic context of bla KPC has revealed that this gene is mostly localized into a class 2 transposon named Tn 4401 ( 12 ). (cdc.gov)
Structure2
- Solution structure of the catalytic domain of gammadelta resolvase. (edu.pl)
- Transposons are more complex in structure than IS elements. (microbiologynotes.org)
MeSH1
- Transposon Resolvases" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (ucdenver.edu)
Circular1
- The enzymes then catalyze the double strand cleavage, exchange of double strands and rejoining of DNA helices so that the DNA transposon is formed into a circular PLASMID. (ucdenver.edu)
Complex1
- A transposon (Tn) is more complex than IS elements. (exama2z.in)