Mechanisms Of Conservative And Replicative Transposition Biology Essay
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Bacteriophage Mu is a temperate phage which adopts transposition pathway in its life cycle. Mu has the capability to integrate into numerous sites in host Escherichia coli genome and cause mutations due to its insertional activation. Mu transposes via two major pathways; conservative and replicative transposition though the molecular switch between the two mechanisms remain unknown. This review will focus on the comparisons between replicative and conservative transposition. The first part will discuss the similarities between the two mechanisms; donor DNA cleavage step and strand transfer step which involves nucleophilic attacks, generating single-strand nicks in Mu DNA and joining it to target DNA via one-step transesterification mechanism. The latter part will concentrate on the different characteristics in each transposition mechanism; in replicative transposition, the end product is duplication of transposon copy in both target and host DNA while in conservative transposition, a simple insertion of transposon is produced in the target DNA.
1. Characteristics of bacteriophage Mu
Phage, derived from the Greek word phagein, literally means "to eat". Bacteriophage Mu was named as such(find out who did) due its nature of infecting and inducing high levels of mutation in host bacteria Escherichia coli., hence the name "Mu" for mutator. The dual nature of Mu - transposon and virus - has made it as the archetypal model of studying phage genetics. Bacteriophage Mu is a temperate phage of E. coli which employs the transposition mechanism in its life cycle. Transposition can either be conservative (excising the transposon and inserting it into bacterial chromosome) or replicative (transposon copies are produced in both transposon and bacterial chromosome). Both mechanisms will be discussed extensively later in this article. Unlike the phage Î», insertion of Mu genome into the target site proceeds in a randomly manner which makes it an excellent mutator.
Fig. 1: The life cycle of bacteriophage Mu(5).
The life cycle of phage Mu is shown schematically in Fig. 1 above. Bacteriophage Mu infect susceptible host cell by adsorption and then, injects its linear viral genome. Once inside the host cell, the linear genome does not circularized(4,5,19), unlike in phage Î». In either case of lytic or lysogenic phase, Mu integrates its DNA into the host genome via conservative transposition(16,19). This is observed differently in phage Î» where the infecting phage DNA will be integrated into host genome only during lysogenization(19). An enzyme called transposase, encoded by MuA gene in the phage genome, is absolutely crucial to carry out this conservative transposition step. Phage DNA is inserted at multiple sites in a bacterial genome which lead to the assumption that the insertion occur by a random manner(8). However, there are several factors that influence target site selection such as MuA protein efficiency and transposition immunity(15).
After integration, Mu usually adopts a quiescent prophage lifestyle(lysogenic phase). The preference between lysogenic and lytic phase in Mu life cycle is dependent on its stability in the lysogen and lysogenic repressors. However, lysogens of Mu phage sometimes enter the lytic phase though this is a rare event. When induced, usually by using temperature-sensitive repressor mutants of phage Mu and subject it at 42ËšC, the lysogen will enter lytic cycle. When the lysogenic repressor is inactivated, Mu transposes via replicative transposition, producing copies of phage genome which will be packaged into new virions. The virions then lyse the host cell and infect new hosts. Bacteriophage Mu virions comprised of icosahedral head(diameter 54nm), a baseplate, a contractile tail and six short tail fibres(5).
Fig. 2: Simplified cartoon illustrating packaging of Mu genome. Typical length of phage Mu DNA is approximately 37kb long. Additional 2 kb of host DNA is incorporated during DNA packaging which is shown as flanking each end of the integrated Mu genome, with most of it at the right end. Unique sequences of host DNA and at the right end of the packaged DNA is dependent on initiation site of packaging in the host DNA(24).
Fig. 3: Physical and genetic map of bacteriophage Mu. Solid black lines represent Mu DNA while the boxes at the two ends indicate flanking host DNA sequences. Mu genes (indicated in block letters) and their corresponding translational products are as indicated(19).
A typical size of wild-type phage Mu DNA is about 37.5 kb, however each phage capsid can accommodate up to 39 kb long. Phage genome has a pac site which serves as the starting point in packaging of the phage DNA, located within attL(5). The initiation cleavage by phage enzyme terminase occurs upstream of the phage pac site, which includes host sequence of about 50-150bp flanking the left end. Second cleavage initiated when a complete filling of capsid is achieved, which includes 0.5 kb to 2 kb of host sequence flanking the right end(1). Genetic and physical map of phage Mu is illustrated in Fig. 3. Bacteriophage Mu utilizes 'headful' mechanism strategy, which confer variable lengths of host DNA flanking the left ends of Mu DNA depending on the initiation site of genome packaging(Fig. 2).
2. Transposition mechanism
Fig. 4: Modes of bacteriophage Mu transposition. (A), (B) and (C) are the common steps in both conservative and replicative transposition of phage Mu. In conservative and replicative transposition, phage Mu will follow-up step (D) and (E) respectively. Curved arrows indicate nucleophile attack, transferring the 3'-OH ends to the staggered 5'-phosphate ends of target DNA. Dentate lines (XXXX) indicate target DNA sequences which are duplicated during transposition (16).
Numerous in vitro studies have been conducted to study the mechanism of transposition, and usually mini-Mu elements are used. A minimal Mu element consists of a selectable gene, a plasmid replication origin and essential Mu ends(2). The mechanism of transposition is discussed in respect to an in vitro system from this point onwards unless stated otherwise. Following discussion on transposition mechanism are based on Shapiro model(22) as it has been widely accepted as the 'golden' model in this field.
The current known modes of transposition is divided into two: non-replicative (conservative) and replicative transposition. Both strategies utilize the same mechanism up to point (Fig. 4C) where each strategy employs different mechanism, producing different end products. A simple insertion of transposon is generated in target DNA by conservative transposition (Fig. 4D) while two copies of transposon formed in both donor and target DNA by replicative transposition (Fig. 4E). Point A to C are considered as the similar features in both conservative and replicative transposition while point D and E is the distinction between the two modes of transposition. Therefore, mechanisms involved in point A,B and C are discussed in context of both replicative and conservative transposition, which comprises of DNA cleavage step and strand transfer step. Sequential stages of both cleavage and strand transfer steps are illustrated in Fig. 4.
2.1 Donor DNA cleavage step
Two critical chemical steps in both transposition pathways are donor DNA cleavage step and DNA strand transfer step(5,8). The donor DNA cleavage step is initiated when water molecules within an active site act as nucleophiles, and attack phosphodiester bond in DNA backbone at each of the transposon end(4,5). The cleavage step involves a direct hydrolysis of phosphodiester bond by water, and not by covalent enzyme-DNA intermediate(17). The phosphodiester bond is cleaved at the flanking host-transposon DNA boundary. 3'-hydroxyl (OH) ends of the Mu DNA are exposed at the end of the cleavage step. Strand transfer results in fusion of target and donor DNA, which forms an intermediate molecule (8). The process (simplified in Fig. 4C) follows the Shapiro model(22).
Bacteriophage-encoded proteins, MuA protein (transposase) and MuB protein (ATPase) are required for transposition. Other requirements to ensure efficiency of transposition are accessory proteins such as host-encoded DNA bending proteins called hydroxyurea (HU) and integration host factor (IHF)(8). The inverted repeats at the end of donor DNA, and target sequence on bacterial chromosome are also important in transposition mechanism. The assembly of higher order protein-DNA complexes called transposome has been identified by in vitro studies(6).
A three-site synaptic complex called the LER complex comprising right and left ends of Mu and transpositional enhancer, was formed in the beginning of transposition in vitro(23). MuA protein binds to MuA binding site at the ends of Mu DNA as monomer, and subsequently function as tetramer of MuA (transposase). Host IHF and HU protein were found to aid in formation and stabilisation of LER complex.
The LER complex is relatively unstable and so, is rapidly converted into stable synaptic complex (SSC), also known as type 0 complex(17). This is the critical checkpoint before any chemical reaction is carried out as it is the rate-limiting step of cleavage reaction(6). A stable synapse between tetramer of MuA and the two ends of Mu DNA is made but no cleavage is initiated yet at this point. Nonetheless, the active site is structurally occupied to the region around the scissile phosphate while the flanking DNA are destabilized upon formation of the SSC complex(6). In addition to formation of a stable synapse, the Mu ends needs to be properly-oriented, a super coiled DNA topology, and accessory DNA sites are also important to proceed to the next step. Formation of SSC usually is short-lived in presence of Mg2+ but can be accumulated in presence of suitable divalent cations such as Ca2+,which promotes the formation of SSC(8,17).
Next, SSC is converted into a type 1 transposome complex, also called as cleaved donor complex(CDC)(9). The 3' ends of Mu DNA are nicked in presence of Mg2+. Two subunits of MuA tetramer, that are associated with the sites that undergo cleavage, assemble in trans arrangement which favours the strand transfer reaction(5). The formation of CDC can then be thought as the result of donor DNA cleavage step. Type 1 transposome complex exhibits greater stability than the type 0 complex though MuA forms structural and functional core in both transposome complexes(6). In addition of stably bound tetramer of MuA proteins, there are loosely associated MuA proteins present in the CDC as well. In absence of MuB protein, MuA tetramer is unable to promote strand transfer reaction unless these extra MuA proteins are present. MuB protein is an ATP-dependent DNA-binding protein, which also acts as an allosteric activator of Mu transposase (MuA proteins)(21). Transposition can still proceed in absence of MuB proteins, but MuA protein by itself is only 1% efficient(3).
2.2 Strand transfer step
A hallmark of this step is the formation of strand transfer complex (STC), also known as type 2 transposome complex. The end product of STC is formation of a branched molecule(Shapiro intermediate) which is characterized by a covalent interaction between donor DNA and target DNA via 5bp single-stranded gaps and its Î¸ structure(22). MuB protein first captures a target molecule and bring it to the vicinity of the transposome complex, forming a TC complex(6). Formation of TC complexes rapidly undergo one-step transesterification reaction, which is the rate-limiting step in the strand transfer step. Interestingly, recruiting of target molecules by MuB proteins and formation of TC complexes can occur at several time point during the reaction pathway(6). This is a particularly efficient step to maximize transposition potential as it would speed up rate of strand transfers during transposition.
The free 3'-OH ends produced from the cleavage step act as nucleophile and attack phosphates of target DNA at the 5' ends. 5-nucleotides long offset nicks are made in the target DNA, generating a staggered arrangement(3). At this stage, the MuA proteins(transposase) are still tightly bound to the branched molecule with single stranded gaps. This pose an obstruction for the assembly of replication fork by host replication factors. The structure of the branched molecule is simplified in (C) of Fig. 4.
The forming of this intermediate molecule serves as the critical point which distinguish between conservative and replicative transposition. A widely accepted model is that the resolving of this co-integrate molecule by a special resolvase complex leads to double copies of transposon being made in both donor and target site(REFerence). This is by definition, a replicative transposition pathway. Thus, the strand transfer complex is destabilized and disassembled by a system of eight E. coli host molecular proteins (DnaB helicase, DnaC protein, DnaG primase, DNA polymerase II, single-strand binding protein, DNA gyrase, DNA polymerase I and DNA ligase) and molecular chaperon called ClpX, producing cointegrates(13).
This transition from transposome complex to a replisome results in duplication of 5-bp target DNA sequences flanking both ends of Mu DNA. Alternatively, if the bacteriophage Mu is to enter the conservative pathway, the co-integrate molecule is repaired or processed without performing Mu DNA replication. The end product of STC in a conservative transposition is a simple insertion of single mini-Mu element inserted into the target DNA(8). However, the mechanism of this model is poorly understood.
Fig. 5: Transposome complexes involved during DNA cleavage complex and DNA strand transfer. (A) A plasmid (gray line) bearing donor mini-Mu element (black line) DNA in the in vitro system is negatively coiled. (B) In presence of host HU protein, Mu A protein bind to the two ends of Mu DNA forming a stable synaptic complex (not shown). Assembly of MuA tetramer produces a nick at each ends of Mu DNA, creating a cleaved donor complex (CDC). (C) Nicked 3' ends of Mu DNA are joined together to target DNA in presence of MuB protein forming a strand transfer complex (STC). MuA tetramer is still tightly bound to the Mu ends in the STC. (D) In replicative transposition, a cointegrate molecule is produced when replication of target DNA initiated from the 3' Mu ends by host replication machinery (13).
3. Replicative transposition
Replicative transposition was first suggested by Ljungquist and Bukhari (1977) to occur in situ after induction of lysogens, which means that the Mu prophage was not excised from host chromosome during transposition(14). The lysogens were digested with restriction enzymes which cleaves both host and Mu DNA at specific restriction sites. Two of the fragments from the restriction digests contain both host and Mu DNA, which corresponds to junctions between host and prophage DNA, suggesting that prophage DNA is replicated in situ of host chromosome(19). Several genetic and biochemical predictions made in the Shapiro model have been demonstrated in both in vivo and in vitro studies, hence this model is accepted as a plausible mechanism to explain transposition in phage Mu.
Numerous techniques have been done to study the direction of replication of Mu DNA during transposition. Results obtained by annealing of Okazaki fragments to separated strands of Mu DNA shows that more than 80% of Mu molecules replication proceed from left to right end(11,19). Electron microscopical observation of mini-Mu element shows that replicating molecules in vitro replicate from both ends in 'equal probability'(11,19). Replication of Mu DNA is accepted to be predominantly unidirectional, that is from left towards the right end(20). Intramolecular replication pathway can result in inversion, deletion, and simple insertion while intermolecular events can produce co-integrate molecules(19). In the case of Mu transposition, formation of co-integrate molecule needs to be resolved in order to produce two replicons; one molecule contains transposon and target DNA while another molecule contains transposon and donor DNA(10).
4. Conservative transposition
The main characteristic of conservative transposition is that phage DNA is not replicated prior to integration. Upon infection of a susceptible host cell (usually E. coli), Mu employs conservative, or also called non-replicative transposition to transfer its genome to the target site. As discussed earlier, conservative transposition pathway follows single strand nicks at the 3' ends of Mu DNA, of which the exposed 3'-OH ends join to the staggered cut target DNA at the 5'ends forming a co-integrate molecule. The co-integrate or so-called Shapiro intermediate is repaired and generates a simple insertion in the target DNA though the mechanism is still poorly understood.
Shapiro model emphasized on single-stranded nicks at Mu ends, joining of Mu to a staggered double-strand break in target DNA, formation of an intermediate molecule, and shedding of heterogeneous of previous host DNA sequences after ligation in conservative pathway(22). On the other hand, Morisato and Kleckner (1984) proposed a different mechanism based on results with Tn10 transposition. Their model is double-stranded cleavages at the transposon ends generating an excised transposon, which then circularizes via ligation on one of the strands(18). It predicts shedding of host sequences from the Mu DNA ends before ligation into the new target DNA. Study of Mu transposition using plasmid substrates in vitro produced results in favour of the Shapiro model, and hence this model has been widely accepted and used in studies.
Fig. 6: A model of conservative transposition which utilizes double-strand cleavages during integration. (A) Transposase bind to the inverted repeats at Mu-host boundary sites and cleaves off the transposon away. (B) Transposase made a staggered cut at target sequence of which exposed 3'-OH ends of transposon attacks 5'-phosphate ends of the host (not shown). The transposon then joins to the host sequence. Duplicated target sequence of 5-bp are completed by host replication machinery (7).
The debate on single-strand or double-strand cleavage however does not end there. If phage Mu were to utilize the Shapiro model of transposition during integration (the well-established cointegrate mechanism), the flanking host sequences would remain bound to Mu ends. This would clearly pose a problem as subsequent target-primed replication of the linear integrant would not work, or simply break the chromosome(1). Evidently, results from in vitro experiments are against this as the transposition end products contain transposon, suggesting a complete transposition process have been accomplished. So, does the infecting Mu DNA utilize the Shapiro model where the cointegrate molecule gets processed and repaired, prior to replication at the flanking sequence? Or does it follow a cut-and-paste mechanism where both strands of Mu DNA gets cleaved off from the flanking host DNA sequence (as illustrated in Fig. 6), where no cointegrate molecule is generated, which eventually means, there is no need for resolve by replication?
An in vitro experiment was done by Au et al. (2006) to observe the fate of flanking host DNA sequences upon phage Mu infection. Specific markers specific to the infecting phage Mu DNA as well as the donor host (lacZ/proB) were used. These markers were acquired from the host in which the phage had been propagated but absent in the host being infected(1). Upon infection of plasmids by bacteriophage Mu, signal for flanking sequences and Mu DNA were detected in the chromosome at the same time point (approximately at minute 8), which correspond to the integration time point of Mu. Subsequent expression of lacZ and proB were detected maximally at minute 15, significantly reduced at minute 30 and by minute 50, expression were halted(1). Maximal expression at minute 15 most likely corresponds to climax of integration of the infecting phage population. These findings strongly suggest that flanking sequences get integrated together with Mu DNA into the new target site and are subsequently, removed by a special mechanism(which explained the undetectable expression at minute 50). This then proves that infecting phage Mu employs an alternate cointegrate mechanism (also called as nick-join-process mechanism) in conservative transposition pathway, where the Mu DNA undergo single-strand nicks, joins to the target DNA, and repaired before replication of the 5-bp gap left by the flanking sequence(1). The mechanism of removal and repair of host flanking sequence however, remains ambiguous.
Dual nature of bacteriophage Mu, a transposable element and a virus, is certainly interesting but what is more fascinating is that it utilizes both replicative and non-replicative transposition throughout its life cycle. The former mechanism produces a transposon copy in both donor and target DNA while the latter usually generates a simple insertion of transposon in the target DNA, leaving a gap in the host DNA which most likely will get degraded.
In the early stages, both replicative and conservative transposition pathway share a similar mechanism. Regardless of the transposition pathway, infecting Mu DNA during the first round of infection will integrate its DNA into the target chromosome via two critical steps; donor DNA cleavage step and strand transfer step. Mu uses a phosphoryl transfer involving nucleophilic attacks of water on phosphodiester bonds of Mu DNA, producing single-strand nicks. A second nucleophilic attack by exposed 3'-ends of Mu DNA on 5'-ends of target phosphodiester bonds, which then joins the Mu DNA to target DNA via one-step transesterification mechanism. A series of transposome complexes are formed throughout these processes including Mu-encoded MuA proteins(transposase) and MuB proteins(ATPase). A cointegrate is produced in both pathways but in replicative transposition, this intermediate molecule is resolved producing two replicons with transposon copy in each molecule. In conservative transposition, the cointegrate is repaired generating a simple insertion in the target DNA. Hence, it is more accurate to name conservative transposition as 'nick-join-process' rather than the conventional 'cut-and-paste' mechanism as the latter suggest double-strand nicks at the transposon end, which has been proven inaccurate by in vitro experiments. Both transposition pathways have been compared extensively in this review but much of functional core of the mechanisms remain to be understood.
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