Linear DNA is vulnerable to exonuclease degradation and suffers from genetic loss due to the end replication problem. Eukaryotes overcome these problems by locating repetitive telomere sequences at the end of each chromosome. In humans and other vertebrates this noncoding terminal sequence is repeated between hundreds and thousands of times, ensuring important genetic information is protected. In most prokaryotes, the end-replication problem is solved by utilizing circular DNA molecules as chromosomes. However, some phage and bacteria do store genetic information in linear constructs, and the ends of these structures form either invertrons or hairpin telomeres. Hairpin telomere formation is catalyzed by a protelomerase, a unique protein that modifies DNA by a two-step transesterification reaction, proceeding via a covalent protein bound intermediate. The specifics of this mechanism are largely unknown and conflicting data suggests variations occur between different systems. These proteins, and the DNA constructs they produce, have valuable applications in the biotechnology industry. They are also an essential component of some human pathogens, an increased understanding of how they operate is therefore of fundamental importance. Although this review will focus on phage encoded protelomerase, protelomerases found from Agrobacterium and Borellia will be discussed in terms of mechanism of action.
- telomere resolvase
- linear plasmid
- doggybone DNA
- Touchlight Genetics
The study of DNA, its structure and how it is replicated has been intensifying since the 1900s. Recent advances in DNA sequencing, bioinformatics and high-resolution imaging has increased our understanding of the variations that exist between different DNA replication systems. In general, the genetic material of bacterial cells is in the form of circular DNA molecules. Infecting bacteriophage may integrate their DNA into the host genome, or maintain it independently as a viral episome; usually this plasmid is also circular. These structures have no free ends and are therefore not susceptible to exonuclease degradation and do not suffer from the end replication problem, whereby genetic material at the tip of a chromosome is lost during each round of replication. However, some prokaryotic cells have been identified as harboring closed linear DNA chromosomes. The ends of these structures are protected by either invertron or hairpin telomeres. Invertron telomeres consist of inverted terminal repeats and covalently attached capping proteins, essential for priming DNA replication. These structures are distinct from hairpin telomeres, which have covalently closed hairpin ends.
The first linear genome of prokaryotes was obtained in 1964, when V. Ravin isolated the
In addition to phage, these unusual enzymes have been isolated from certain bacteria. The best studied being ResT from
Although currently under debate, it has been suggested protelomerases are tyrosine-recombinase-like enzymes. It remains to be determined whether the bacterial protelomerases have their origin in phage as both, to some extent, share a common substrate recognition and a DNA cleavage/rejoining mechanism. In addition, some protelomerases have been identified as having roles in vivo unrelated to telomere resolution such as single strand annealing  and ATP-dependent helicase activities . Further research into this important class of enzymes should help elucidate the significance of single strand annealing and DNA unwinding activities during closed linear chromosome replication.
Not only are protelomerases essential for the organisms in which they reside, but their unique functionality makes them valuable to the biotechnology industry. DNA constructs produced using protelomerase are being marketed by Lucigen as improved cloning vectors for highly repetitive sequences [10, 11]. Linear structures are not susceptible to supercoiling, thus making them more stable and less susceptible to genetic loss during replication . Protelomerases can also be expressed in engineered
There is high interest in the study of this protein family due to their utility and potential value for biotechnology. To date, research has largely focused on characterizing protelomerase recognition sequences, solving 3-dimensional structures and exploring the effects of protein mutations on activity. An improved understanding of how protelomerases function will enhance their value for applications in synthetic biology, and may provide the opportunity to invent new and novel applications.
2. Mechanism of telomere resolution
Despite the diversity of organisms in which protelomerases reside, important features have been identified that unify and define this class of protein. The protelomerase target site, denoted as
Current models propose that protelomerases bind nonspecifically to DNA and scan the sequence until finding the target site, or coming into contact with another monomer, at which point the protein immobilizes . Immobilization occurs upon dimerization, whether this forms at the substrate target sequence or not. However, only when at the correct site will the reaction of telomere formation be catalyzed. This phenomenon can be observed in vitro, where a high concentration of TelK (over 400 nm) results in the condensation of DNA and inhibition of telomere formation . Protelomerase concentration in vivo therefore, must be carefully controlled. This notion has been explored in phage N15, where negative control is used to regulate the levels of protein .
Protelomerases catalyzes a two-step transesterification reaction, and all are thought to initiate DNA cleavage using an active site tyrosine residue. This residue performs nucleophilic attack on the phosphodiester bond to form a 3′ covalently attached protein-DNA intermediate and a free 5′-OH. The protein bound intermediate is vital for avoiding deleterious double strand breaks and prevents the premature abortion of reactions . The DNA cleavage reaction happens in a staggered formation 3-bp either side of the symmetrical target site center. This leaves a 6-nucleotide overhang that loops back and is ligated to form the covalently closed hairpin end. The DNA cleaving and re-joining reactions are isoenergetic and, in principle, each step in the reaction is reversible . As DNA hairpins are unable to form complete base pairings , they are less stable than the starting material. In this case directionality is determined by the loop processing step. This part of the reaction is poorly understood and data available indicates conflicting mechanisms in different systems.
Figure 1a is a model for telomere resolution by the protelomerase TelK from phage φKO2. An interlocked protein dimer forms at the
3. Substrate sequences
Identifying the natural target site of protelomerases is not straightforward. A logical strategy is to determine the nucleotide sequence of the resultant telomere and deduce from this the starting material. However, sequencing telomeres is notoriously difficult as the hairpin ends are incapable of ligating to the vector during sequencing library construction . An adapted method has been used, whereby a nuclease opens the closed ends to make them compliant for ligation . This does not always give absolute results, but can provide predictions for the target sequences, which may be confirmed by in vitro studies .
In general, protelomerases are highly specific and only process one target sequence. The exception to this is ResT, which is far less stringent and can resolve nine different telomere sequences found in the
Comparison of the TelN and TelK
3.1 Minimal substrate
In vitro studies have also involved truncating target sites in order to identify the minimum sequence required for protelomerase binding and telomere resolution. To date, the minimal site identified that can be resolved, is a 26-bp substrate of TelA . This was found by systematically deleting residues from both sides of the target sequence, until no product was produced. Similar studies have been performed on the TelN substrate. Figure 2 shows the complete telomere occupancy (
4. Linear genomes
In order to further appreciate how protelomerases function, it is necessary to understand their role in relation to the whole phage or bacterial cell life-cycle. Bacteriophage N15 has been extensively characterised and Figure 3 illustrates the different structures its genetic material forms upon infection of
5. Bacteriophage N15 replication
Various models have been proposed to describe the replication and processing of linear DNA with hairpin telomeres . Uncertainties arise about the specific mode of replication and whether it occurs uni- or bi-directionally. Other important factors that need to be determined are, where in the plasmid replication is initiated from and what the replication intermediates are. Bacteriophage N15 can be used as the model system to explore these questions, the general organization of its genome is shown in Figure 4. Genes have been largely identified by homology inferred from sequence similarity to other bacteriophages; mainly lambda, HK97 and HK002 . The division between the left- and right-hand side of the N15 genome is marked by
Figure 5 describes how these linear N15 constructs may be replicated and processed; it is consistent with the data cited above and proposes structures that have been validated by electron microscopy . In pathway A, following replication of the
5.1 Lytic replication
A model of how N15 lytic replication could occur is proposed in pathway C of Figure 2. The DNA is duplicated and resolved into two circular monomers, as opposed to linear structures. These circular molecules are the starting material for subsequent cycles of amplification. This style of lytic replication is similar to that of phage lambda. This bacteriophage also circularizes its DNA upon entering the host cell, it has
The key difference between N15 and lambda bacteriophage is that lambda integrates its DNA into the host genome, whereas N15 does not. Although protelomerases share some sequence homology with lambda integrases, and both appear to have comparable roles in helping establish prophage DNA, these proteins are not functional analogues. During lytic replication the lambda integrase is dispensable, in comparison the protelomerase of N15 is essential. This phenomenon has been proven by experiments showing N15 deficient in protelomerases are incapable of infecting
5.2 N15 as a model for the replication of other linear plasmids
To what extent can the model of bacteriophage N15 be extended to describe the replication of other replicons with hairpin ends? Genomic sequence analysis of phage encoded protelomerases reveal little overall sequence similarity . However, the organization of functional domains is analogous and they appear to have conserved regulatory regions . This would suggest a shared mechanism of plasmid replication and lysogeny control . Virions of φKO2, VP58.5, VP882 and PY54 have cohesive ends [27, 29, 2], which facilitate circularization and enable the formation of similar structures as those described for N15. The absence of
Further comparisons can be made between the suggested phage model and that of bacterial linear chromosome replication.
6. Structural data
6.1 X-ray crystallography
The X-ray structures described for both TelK and TelA have greatly enhanced our understanding of the protelomerase mechanism [21, 22]. The structure of TelK (from phage φKO2), is shown in Figure 6; crystallized in a dimer conformation complexed with the minimal cognate DNA sequence of 44-bp [PDB: 2V6E]. TelK has been divided into three core domains, all of which make contact with the DNA. These include, the muzzle at the N-terminus, the catalytic domain in the center, and the stirrup domain at the C-terminus. A long alpha-helical linker is also highlighted, and this connects the core catalytic and N-terminal domains.
One of the most striking observations of this structure is the level distortion: DNA is bent at roughly 73° parallel to the axis of symmetry . This provides a valuable insight into the mechanism of telomere resolution by TelK and would appear to refute previous theories that the DNA is forced into a cruciform conformation . Core substrate binding occurs at the N-terminus and the muzzle makes extensive contacts with the opposite subunit, strengthening the protein’s structure and pushing the DNA into this strained conformation. The catalytic site is formed at the dimer interface, it binds to the opposite side of the substrate relative to the N-terminus and the helical linker that connects these two domains is fixed in the major groove. Extensive electrostatic interactions mediate the interaction.
Closer examination of the interactions between the DNA and protein reveal seven nucleotides that form hydrogen bonds with nearby residues (shown in cyan in Figure 7) and are presumed key for substrate recognition. This model is supported by the previously cited studies, whereby the natural PY54 substrate was effectively mutated into a sequence that could be processed by TelK. Adenine at position 42 is circled; this is one of the bases identified as forming hydrogen bonds with TelK and is one of the points that required mutating in order to form a cognate sequence. High salt has been shown to inhibit telomere resolution by protelomerases , this is possibly reflected by the extensive hydrophilic protein-DNA interactions that would be disrupted by an excess of ions.
The stirrup domain of TelK has a winged helix-turn-helix motif , it makes few contacts with the rest of the protein but extends the DNA binding interface. In stabilizing the strained substrate conformation, this part of the protein aids hairpin formation; however, it is nonessential for the cleavage reaction . Following strand cleavage, the stored energy is released, and this drives dimer dissolution which is proceeded by spontaneous hairpin formation. The stirrup is not conserved among protelomerases and this provides further evidence to support the theory that the mechanism of telomere resolution varies between different systems.
The structure of the bacterial protelomerase, TelA has also been described via X-ray crystallography. TelA is considerably smaller than TelK, it lacks the stirrup and only consists of the catalytic and N-terminal domains. This design is similar to that of tyrosine recombinases, which are also typically composed of two domains . The N-terminal 100 residues are poorly resolved in comparison to the rest of the protein, this area of low electron density suggests flexibility of the polypeptide chain. Comparing dimer substrate complexes of TelA to those of TelK (Figure 8) reveals a similar DNA conformation at the dimer interface. Extensive hydrogen bonds and van der Waals interactions are also involved in dictating the substrate specificity of TelA and the DNA exhibits the same disjunction down its helical axis .
6.2 Catalytic domain
The catalytic domain of TelK is a mixed alpha beta structure. Figure 9 shows the core catalytic residues of TelK R275, K300, K380, R383 and H416. These act together to maintain catalytic activity and coordinate nucleophilic attack of the tyrosine. Side chains of the basic amino acids at positions one, three and four provide a hydrogen bonding network that coordinates the scissile phosphate and stabilizes the transition state . In type IB topoisomerases, the pentad is usually composed of RKKRH/N , with basic residues 1 and 3 having the same stabilization effect. In these proteins, the second lysine residue has been shown to donate a proton to the 5′-OH leaving group, which aids its removal during cleavage . It is feasible that the lysine in the protelomerase’s active site, with its side chain positioned between the DNA O5’ and nonbridging oxygen, also functions in this way and protonates the leaving group .
These crystal structures are invaluable when trying to decipher the mechanism of protelomerase-catalyzed telomere resolution. TelN and TelK have highly homologous sequences and can process the same target site , it is therefore likely the structures of these enzymes are analogous and information about TelN can be derived from examining the TelK structure. However, is important to note that the crystallized structure of TelK is not full length and lacks 100 residues from the C-terminus. This does not appear to significantly affect protein activity in vitro , but the significance in vivo is unconfirmed.
7. Evolutionary history
It is widely believed Tyrosine recombinases and type IB topoisomerases have arisen from a common ancestor . These structurally and mechanically analogous proteins catalyze important DNA rearrangements, they use an active site tyrosine residue and form covalently bound protein-DNA intermediates. Similarities between this mechanism, and that of protelomerases, has led to the suggestion that these protein classes have a shared evolutionary relationship .
Key to the function of tyrosine recombinases is the conserved catalytic motif: “RKHRH” [52, 53]. Crystal structures and sequence alignments reveal that protelomerases share this catalytic pentad , with exception of the middle residue, which varies between systems. Deviation at this central point is also observed in tyrosine recombinases, where the central histidine may be replaced by an arginine, asparagine, lysine or tyrosine. In protelomerases; TelN and TelK both have a methionine at this position, PY54 contains a lysine, VHML has a histidine and the bacterial protelomerases of
Structural comparisons outside of the catalytic domain reveal low overall sequence homology at both the N- and C- terminus. ResT is smaller than the phage proteins, partial proteolysis separates the 449 amino acid protein into two domains , and sequence analysis predicts its architecture is more comparable to that typical of tyrosine recombinases. In addition, this protein has the unusual and surprising ability to synapse Holliday Junctions . The reaction appears to be favored in conditions that are counterproductive to telomere resolution, such as negative supercoiling, or unsymmetrical
In ResT, additional catalytic residues outside of the core pentad are required for telomere resolution . This indicates digression from a typical tyrosine recombinase type mechanism. Furthermore, mutation of ResT histidine 324, the fifth residue of the catalytic motif does not result in total loss of activity . This would mark an obvious disparity between these two classes of enzymes, if it was not for the observation that this residue is also not essential in Flp recombinases . Here it appears the final amino acid has a structural rather than catalytic role , which could be mirrored in ResT.
Analysis of the DNA substrates reveal further fundamental differences between protelomerases and tyrosine recombinases. Aside from ResT, which it has been suggested can act on more than one target site, protelomerases are specific and have stringent substrate sequence requirements. The target site of one recombinase often includes many other related points, such as phage or bacterial attachment sites. Furthermore, the reaction is intramolecular and can require auxiliary proteins . This implies a mechanism more involved and complex than that of telomere resolution. The reaction catalyzed by type IB topoisomerases is considerably simpler, as these proteins act as monomers  and do not display the same sequence specificity as protelomerases.
In conclusion, there are key differences between the catalytic mechanism of protelomerases and tyrosine recombinases/type IB topoisomerases. However, there are also significant similarities and whether these proteins have evolved from a common ancestor is difficult to determine. It is expected that the conversion of a tyrosine recombinase to an enzyme capable of telomere resolution would be accompanied by the linearization of plasmid DNA . The data suggesting this could be achieved with relative ease adds support to the argument these proteins are related. Under certain conditions, recombinases can have topoisomerase activity, and topoisomerases can affect DNA strand exchanges . This raises an interesting question as to whether protelomerases, under the correct conditions, may also be able to exhibit topoisomerase activity .
8. Applications in biotechnology
The unique properties of protelomerases, and the DNA structures they produce, makes them a valuable class of protein that have important applications in synthetic biology and biotechnology. Linear DNA does not exhibit the supercoiling associated with plasmids, as the ends are free to rotate. This makes them stable vectors invaluable for cloning difficult sequences. DNA that is rich in adenine and thymidine, or contains lots of short tandem repeats is typically hard, if not impossible, to clone into circular vectors . A commercially available cloning vector, pJAZZ from Lucigen, is based on the linear N15 phage genome. pJAZZ is sold as part of a cloning system (BigEasy Kit), enabling the insertion of otherwise unclonable sequences into the vector for the creation of viable linear plasmids that can be transformed into cells. pJAZZ vectors encode RepA and TelN, essential for bidirectional replication and telomere resolution. Transcriptional terminators flank the cloning site, thus minimizing interference and preventing transcription into and out of this region. These modifications extend the cloning possibilities and allow for the insertion of large cDNAs or operons .
The pJAZZ system has been further modified to specifically enhance its efficiency for the production of in vitro transcribed (IVT) mRNA. IVT mRNA is a powerful therapeutic tool, enabling the transient expression of heterologous proteins [61, 62]. However, in order to optimize translation efficiency and mRNA stability, the poly(A) tail length of the mRNA needs to be defined and optimized . In particular, mRNA with poly(A) tails >300 nucleotides and purines at the 3′ end have been demonstrated as highly effective and appear to exhibit improved translation properties compared to those with shorter poly(A) tracts . Due to its linear structure, a pJAZZ derived plasmid, called p(Extended Variable Length) (pEVL), can create poly(A) tracts of up to 500 bps in length. Furthermore, the residues at the 3′ end can be defined as either adenine or guanine. This has a significant advantage over conventional circular DNA, which cannot incorporate more than 174 bp of poly(A) tract without conferring extreme instability .
Mediphage Bioceuticals is a genetic medicine company that has also utilized the unique DNA processing capability of protelomerases for their technology. They have developed a one-step in vivo platform to produce linear covalently closed constructs, called ministring DNA . These constructs are produced in
Another in vivo application of protelomerases has been explored by Katzen at colleagues, who used TelN to fragment an
Touchlight Genetics Ltd. has also utilized protelomerases for their technology. The platform they have developed is a purely in vitro DNA production process that eliminates all the major problems associated with using bacterial fermentation for DNA amplification. Their cell-free technology uses a phage DNA polymerase from Phi29 to produce large amounts of DNA concatemers from small amounts of starting plasmid DNA template. DNA concatemers are processed by the protelomerase TelN, to create linear covalently closed constructs that are marketed as dbDNA. The closed ended linear DNA construct is able to encode long, difficult DNA sequences which are not tolerated in high yield production of plasmid DNA due to selection pressures. The in vitro amplification technology produces DNA containing no bacterial origin of replication sequences or antibiotic selection marker. These vectors are capable of immunizing against influenza infection, with a response comparable to that of plasmid DNA , as well as improving tumor growth control in a Human papillomavirus (HPV) driven head and neck cancer model by delivering a therapeutic vaccine encoding for HPV16 E6 and E7 antigens . Furthermore, dbDNA constructs have been used to generate functional lentiviral vectors  and are promising candidates for the production of recombinant adeno-associated virus (AAV) vectors . This platform could therefore be important for gene therapy [70, 71] and this synthetic process for DNA production will have a broad range of application within the wider synthetic biology field.
Protelomerases are an interesting and unique class of protein. In forming telomeric structures at the ends of linear plasmids, they protect the genetic material from degradation and provide a novel solution to the end replication problem. They have also been implemented as an essential component of certain human pathogens and have important applications in synthetic biology. Despite this, protelomerases remain poorly characterised and many questions about their structure, function, mechanism and evolutionary history remain unanswered.
Much of our current knowledge has been obtained by combining information from crystal structures, analysing sequences and performing in vitro assays with protein and substrate variations. The results of these studies have enabled us to compare the protelomerases from different systems and it is clear that there is much variety within this protein family. In particular, ResT has been identified as having additional, largely unexplainable, functionality aside from telomere resolution. Potentially further characterization of the other protelomerases will lead to similar revelations.
Biochemical analysis of protelomerases from ΦHAP1, PY54 and VP58.2, will shed further light on the underlying properties that differentiate these telomere resolving enzymes. Such work could also explore the evolution of protelomerases and prokaryotes with linear plasmids. Similarities in the genome organization of telomere phage suggest a common ancestor  and whether the bacterial proteins originated from these is currently unknown. Introducing different phage into the same cell and determining their compatibility can give insight into evolutionary background . An understanding of the relationship between phage lambda and telomere phage, in particular N15, will provide an interesting and important insight into how plasmid and phage can interact and evolve.
Crystal structures of TelK and TelA provide a solid starting point for research aiming to solve structures of protelomerases. These can also be used for homology modeling to infer information about proteins with high sequence similarities. Advances in the field of synthetic biology and protein engineering make detailed knowledge of these proteins even more valuable. An increased understanding of how they operate, and which parts are responsible for specific functionalities, will open up opportunities to produce variants with altered activities.
Appendices and nomenclature
TosTelomerase occupancy site
Coscohesive end sites
Oriorigin of replication
IVTin vitro transcribed
pEVLp(Extended Variable Length)
Conflict of interest
SK has recently started a PhD jointly between Touchlight Genetics and Renos Savva; however, this has not relatively biased or affected the content of this chapter.
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