Highly efficient expression of Escherichia coli heat-labile enterotoxin B subunit in plants using potato virus X-based vector

A synthetic gene of the B-subunit of Escherichia coli heat-labile toxin, optimized for expression in plants, was designed and synthesized. The recombinant viral vector was constructed on the basis of potato virus X containing the LTB gene instead of the removed triple block of transport genes and the coat protein gene, which provides for LTB expression in plants. The vector is introduced into the plant cells during cell infiltration by agrobacteria incorporating a binary vector, the T-DNA region of which contains a cDNA copy of the recombinant viral genome. Under conditions of posttranscriptional gene silencing inhibition, the LTB yield in Nicotiana benthamiana plants is 1-2% of total soluble protein; in this case, LTB synthesized in plants forms pentameric complexes analogous to those found in the native toxin. The designed viral system of LTB transient expression can be used to obtain in plants a vaccine against enteropathogenic Escherichia coli.

[Isolation and characteristics of new thermostable DNA ligase from archaea of the genus Thermococcus]

The DNA ligase gene from thermophilic archaea of the genus Thermococcus (strain 1519) was identified and sequenced in the polymerase chain reaction. The recombinant enzyme LigTh1519 was expressed in Escherichia coli, purified, and characterized. LigTh1519 was capable of ligating the cohesive ends and single-strand breaks in double-stranded DNA (ATP as a cofactor). The optimum conditions for the ligase reaction appeared as follows: 100 mM NaCl, 50 mM MgCl2, pH 7.0-10.5, and temperature 70 degrees C. More than 50% Lig1519 activity were preserved after incubation of the enzyme at 80 degrees C for 30 min. New thermostable DNA ligase LihTh1519 may be used for basic and applied researches in molecular biology and genetic engineering.

The 5' untranslated region of the maize alcohol dehydrogenase gene contains an internal ribosome entry site

Adh1, the maize gene encoding alcohol dehydrogenase ADH1, mRNA is efficiently translated in O2-deprived roots of maize, whereas many normal cellular mRNAs are poorly translated. It has been shown that adh, the 5' untranslated region of adh1 mRNA, provides effective translation of mRNA under hypoxia and heat shock conditions in Nicotiana benthamiana plants. We found that adh contains the internal ribosome entry site (IRES) active both in vivo, in N. benthamiana cells, and in vitro, in rabbit reticulocyte lysate translation system. It is widely supposed that cap-independent internal initiation may maintain efficient translation of particular cellular mRNAs under a variety of stresses and other special conditions when cap-dependent protein synthesis is impaired. We evaluated the level of IRES activity of adh and found that its contribution to the overall translation of adh-containing mRNA in plant cells is less than 1% both under normal conditions and under heat shock. The low efficiency of this IRES is inconsistent with its possible role as a main factor ensuring efficient translation of adh1 mRNA under stress conditions.

Complete sequencing of potato virus X new strain genome and construction of viral vector for production of target proteins in plants

The complete nucleotide sequence of the genome of a new potato virus X (PVX) strain Tula isolated by us has been determined. Based on comparison of the PVX Tula nucleotide sequence with the sequences of 12 other PVX strains, this strain was assigned to the European cluster of PVX strains. Phylogenetic analysis revealed the same phylogeny for both full genome sequences and nucleotide sequences of polymerase and coat protein genes, suggesting that the PVX evolution did not involve recombination between different strains. The full-size cDNA copy of the PVX Tula genome was cloned and the accumulation of the viral coat protein in infected Nicotiana benthamiana was shown to be about twofold higher than for the PVX strain UK3. Based on the PVX Tula genome, a new vector which contained the target gene instead of the removed triple transport gene block and the coat protein gene has been constructed for expression of target proteins in plants. The productivity of the new vector was about 1.5-2-fold higher than the productivity of the vector of the same structure based on the standard PVX strain genome. The new viral vector can be used for superproduction of recombinant proteins in plants.

[The 5' untranslated region of the maize alcohol dehydrogenase gene provides efficient translation of mRNA in plants under stress conditions]

Reduced level of expression of most cell proteins under stress conditions is determined by low efficiency of cap-dependent translation of corresponding mRNAs. The maize gene encoding alcohol dehydrogenase, adh1, is an example of a gene which mRNA is efficiently translated under hypoxia. Using reporter gene assay we showed that the leader sequence of adh1 mRNA, provides efficient translation of reporter gene gfp in Nicotiana benthamiana cells under hypoxia and heat shock. The presence of this leader sequence in 5' UTR of mRNA does not change the level of expression in aerobic conditions, but under hypoxia and heat shock the levels of reporter gfp expression were reduced about 5-10 fold in the absence of leader and remained unaffected in its presence in 5'UTR. We found that this leader sequence does not change the level of mRNA stability and does not exhibit promoter activity. Consequently, leader sequence acts as translational enhancer providing efficient translation of mRNA in plant cells under stress conditions. Introduction of this sequence into standard expression cassettes may be used for development of new systems of expression of target proteins in plants, efficient under stress conditions.

The antirepressor needed for induction of linear plasmid-prophage N15 belongs to the SOS regulon

The physiological conditions and molecular interactions that control phage production have been studied in only a few families of temperate phages. We investigated the mechanisms that regulate activation of lytic development in lysogens of coliphage N15, a prophage that is not integrated into the host chromosome but exists as a linear plasmid with covalently closed ends. We identified the N15 antirepressor gene, antC, and showed that its product binds to and acts against the main phage repressor, CB. LexA binds to and represses the promoter of antC. Mitomycin C-stimulated N15 induction required RecA-dependent autocleavage of LexA and expression of AntC protein. Thus, a cellular repressor whose activity is regulated by DNA damage controls N15 prophage induction.

Tightly regulated, high-level expression from controlled copy number vectors based on the replicon of temperate phage N15

A new Escherichia coli host/vector system has been developed to allow a dual regulation of both the plasmid copy number and gene expression. The new pN15E vectors are low copy number plasmids based on the replicon of temperate phage N15, comprising the repA replicase gene and cB repressor gene, controlling the plasmid copy number. Regulation of pN15E copy number is achieved through arabinose-inducible expression of phage N15 antirepressor protein, AntA, whose gene was integrated into the chromosome of the host strain under control of the PBAD promoter. The host strain also carried phage N15 partition operon, sop, allowing stable inheritance of pN15E vectors in the absence of selection pressure. In the first vector, pN15E4, the same PBAD promoter controls expression of a cloned gene. The second vector, pN15E6, carries the phage T5 promoter with a double lac operator repression module thus allowing independent regulation of promoter activity and copy number. Using the lacZ gene to monitor expression in these vectors, we show that the ratio of induction/repression can be about 7600-fold for pN15E4 and more than 15,000-fold for pN15E6. The low copy number of these vectors ensures very low basal level of expression allowing cloning genes encoding toxic products that was demonstrated by the stable maintenance of a gene encoding a restriction endonuclease in pN15E4. The tight control of transcription and the potential to regulate gene activities quantitatively over wide ranges will open up new approaches in the study of gene function in vivo and controlled expression of heterologous genes.

[Initiator protein DnaA of Escherichia coli is a negative replication regulator of the linear phage-plasmid N15]

Temperate bacteriophage N 15 in the lysogenic state is incapable of integrating in the chromosome of Escherichia coli and represents a linear plasmid with covalently closed ends. The phage repA gene, the product of which possesses activities of primase and helicase, ensures replication of N15 DNA. The ori site of initiation of N15 replication contains binding sites for RepA and a potential site of binding the bacterial initiator protein DnaA. It was shown in our work that replication of miniplasmids based on N15 replicon as well as replication of N15 DNA during lytic growth do not depend on DnaA. Moreover, introducing mutations into the potential DnaA binding site increases the copy number of circular and linear miniplasmids that contain repA gene. These data suggest that DnaA is a negative rather than positive regulator of phage N15 replication. This is assumed to be caused by properties of interaction between RepA and DnaA during initiation of N15 replication or by transcriptional silencing of repA gene due to the binding of DnaA to the ori site located within the coding repA sequence.

Functional characterization of the repA replication gene of linear plasmid prophage N15

The prophage of coliphage N15 is not integrated into the chromosome, but exists as a linear plasmid molecule with covalently closed ends. The only phage gene required for replication of circular N15 miniplasmids is repA (gene 37). Here we show that RepA-driven replication of the N15-based circular and linear miniplasmids is independent of host DnaB helicase protein, but requires the host DnaG primase. Replication of phage N15 DNA during lytic growth following infection does not depend on either DnaG or DnaB, but DnaG is required for lytic development after induction of the N15 lysogen. Finally, protein sequence analysis and replication data using different mutant strains suggest that RepA protein combines helicase and primase functions.

[Structural organization and control of expression of the sop-operon of linear plasmid prophage N15]

Stable inheritance of bacterial chromosomes and low-copy-number plasmids depends on the active partition of replicated molecules between daughter cells. The partition mechanism is well known for circular plasmids F and P1. The mechanism of partition of linear replicons was studied with the example of bacteriophage N15, which persists as a linear plasmid with covalently closed ends on lysogeny, rather than integrating into the Escherichia coli chromosome. Since stable inheritance of N15 is due to the sop operon homologous to sop of the F plasmid, the control of expression of the N15 sop genes was analyzed. The sop promoter (Psop) contains a binding site for bacterial IHF and five CTTTGC copies, which overlap the -35 and -10 elements. The Sop proteins were shown to interact with a Psop-containing DNA fragment in vitro. Transcription of the sop operon is regulated by the Sop proteins: SopA represses Psop, and SopB enhances the repression, having no effect on the promoter activity in the absence of SopA. In N15 lysogenic cells, Psop proved to be repressed. This regulatory mechanism was assumed to ensure production of SopA and SopB in amounts required for the segregation stability of N15 and to neutralize occasional fluctuations of their concentration in the cell.

[Expression regulation of the protelomerase gene of the bacteriophage N15]

The N15 bacteriophage, when in the lysogenic state, does not integrate into the chromosome; in fact, it exists as a linear plasmid with the covalently closed ends. Upon infection, the phage DNA circularizes via its cohesive ends, after which a specific enzyme, the N15 protelomerase, cuts the circular molecule thus generating a linear plasmid with the covalently closed telomeres. Protelomerase generates, as the replication of plasmid prophage proceeds, the hairpin telomeres in replicated molecules. We identified the promoter of the protelomerase gene and demonstrated that it could be repressed presumably due to its binding with 3 tosL sites overlapping the promoter. We also found the transformation efficiency of E. coli cells of linear DNA with hairpin telomeres to be approximately 100-fold lower versus the circular DNA of the same size. At the same time, presence of the N15 prophage or of the protelomerase-expressing vector enhances, in a strain being transformed, the efficiency of its transformation by linear DNA up to a level ensured in transformation by circular plasmids. We believe that protelomerase, while binding with the hairpin telomeres, protects the latter from degradation by cellular nucleases.

Bidirectional replication from an internal ori site of the linear N15 plasmid prophage

The prophage of coliphage N15 is not integrated into the chromosome but exists as a linear plasmid molecule with covalently closed hairpin ends (telomeres). Upon infection the injected phage DNA circularizes via its cohesive ends. Then, a phage-encoded enzyme, protelomerase, cuts the circle and forms the hairpin telomeres. N15 protelomerase acts as a telomere-resolving enzyme during prophage DNA replication. We characterized the N15 replicon and found that replication of circular N15 miniplasmids requires only the repA gene, which encodes a multidomain protein homologous to replication proteins of bacterial plasmids replicated by a theta-mechanism. Replication of a linear N15 miniplasmid also requires the protelomerase gene and telomere regions. N15 prophage replication is initiated at an internal ori site located within repA and proceeds bidirectionally. Electron microscopy data suggest that after duplication of the left telomere, protelomerase cuts this site generating Y-shaped molecules. Full replication of the molecule and subsequent resolution of the right telomere then results in two linear plasmid molecules. N15 prophage replication thus appears to follow a mechanism that is distinct from that employed by eukaryotic replicons with this type of telomere and suggests the possibility of evolutionarily independent appearances of prokaryotic and eukaryotic replicons with covalently closed telomeres.

Partition operon expression in the linear plasmid prophage N15 is controlled by both Sop proteins and protelomerase

The temperate coliphage N15, unlike most low copy-number prokaryotic replicons, is maintained as a linear DNA molecule with covalently closed ends. Accurate partitioning of the plasmid prophage is assured by a close homologue of the sop locus of the F plasmid. However, the region upstream of the N15 sopAB genes contains multiple putative promoters, in contrast to F sop whose expression is driven by one negatively autoregulated promoter. In addition, the centromere of N15 is represented by four inverted repeats located at widely separated sites within the region essential for replication and control of lytic functions. We have analysed expression of N15 sop genes. We find that transcription of N15 sop is driven by two major promoters. The first, P1, is similar in sequence and function to the F sop promoter; it is repressed by Sop proteins. The second promoter, P2, is upstream of P1 and is several times stronger. It is insensitive to regulation by Sop proteins but is tightly repressed by protelomerase, the N15 enzyme that completes prophage replication by generating hairpin telomeres. These results establish a regulatory link between the partition system and other processes of N15 maintenance.

Mapping of functional domains in F plasmid partition proteins reveals a bipartite SopB-recognition domain in SopA

Active partition of the F plasmid to dividing daughter cells is assured by interactions between proteins SopA and SopB, and a centromere, sopC. A close homologue of the sop operon is present in the linear prophage N15 and, together with sopC-like sequences, it ensures stability of this replicon. We have exploited this sequence similarity to construct hybrid sop operons with the aim of locating specific interaction determinants within the SopA and SopB proteins that are needed for partition function and for autoregulation of sopAB expression. Centromere binding was found to be specified entirely by a central 25 residue region of SopB strongly predicted to form a helix-turn-helix structure. SopB protein also carries a species-specific SopA-interaction determinant within its N-terminal 45 amino acids, and, as shown by Escherichia coli two-hybrid analysis, a dimerization domain within its C-terminal 75 (F) or 97 (N15) residues. Promoter-operator binding specificity was located within an N-terminal 66 residue region of SopA, which is predicted to contain a helix-turn-helix motif. Two other regions of SopA protein, one next to the ATPase Walker A-box, the other C-terminal, specify interaction with SopB. Yeast two-hybrid analysis indicated that these regions contact SopB directly. Evidence for the involvement of the SopA N terminus in autoinhibition of SopA function was obtained, revealing a possible new aspect of the role of SopB in SopA activation.

Mechanisms of replication and telomere resolution of the linear plasmid prophage N15

The prophage of coliphage N15 is not integrated into the bacterial chromosome but exists as a linear plasmid molecule with covalently closed ends. Upon infection of an Escherichia coli cell, the phage DNA circularizes via cohensive ends. A phage-encoded enzyme, protelomerase, then cuts at another site, telRL, and forms hairpin ends (telomeres). Purified protelomerase alone processes circular and linear plasmid DNA containing the target site telRL to produce linear double-stranded DNA with covalently closed ends in vitro. N15 protelomerase is necessary for replication of the linear prophage through its action as a telomere-resolving enzyme. Replication of circular N15-based miniplasmids requires the only gene repA that encodes multidomain protein homologous to replication proteins of bacterial plasmids replicated by theta-mechanism, particularly, phage P4 alpha-replication protein. Replication of the N15 prophage is initiated at an internal ori site located within repA. Bidirectional replication results in formation of the circular head-to-head, tail-to-tail dimer molecule. Then the N15 protelomerase cuts both duplicated telomeres generating two linear plasmid molecules with covalently closed ends. The N15 prophage replication thus appears to follow the mechanism distinct from that employed by poxviruses and could serve as a model for other prokaryotic replicons with hairpin ends, and particularly, for linear plasmids and chromosomes of Borrelia burgdorferi.

The protelomerase of the phage-plasmid N15 is responsible for its maintenance in linear form

The prophage of coliphage N15 is not integrated into the bacterial chromosome but exists as a linear plasmid molecule with covalently closed ends. Upon infection of an Escherichia coli cell, the phage DNA circularises via cohesive ends. A phage-encoded enzyme, protelomerase, then cuts at another site, telRL, and forms hairpin ends (telomeres). We demonstrate that this enzyme acts in vivo on specific substrates, and show that it is necessary for replication of the linear prophage. We show that protelomerase is an end-resolving enzyme responsible for processing of replicative intermediates. Removal of protelomerase activity resulted in accumulation of replicative intermediates that were found to be circular head-to-head dimers. N15 protelomerase and its target site constitute a functional unit acting on other replicons independently of other phage genes; a mini-F or mini-P1 plasmid carrying this unit replicates as a linear plasmid with covalently closed ends. Our results suggest the following model of N15 prophage DNA replication. Replication is initiated at an internal ori site located close to the left end of plasmid DNA and proceeds bidirectionally. After replication of the left telomere, protelomerase cuts this sequence and forms two hairpin loops telL. After duplication of the right telomere (telR) the same enzyme resolves this sequence producing two linear plasmids. Alternatively, full replication of the linear prophage to form a circular head-to-head dimer may precede protelomerase-mediated formation of hairpin ends.

The anti-immunity system of phage-plasmid N15: identification of the antirepressor gene and its control by a small processed RNA

N15 is a temperate virus of Escherichia coli related to lambdoid phages. However, unlike all other known phages, the N15 prophage is maintained as a low copy number linear DNA molecule with covalently closed ends. The primary immunity system at the immB locus is structurally and functionally comparable to that of lambdoid phages, and encodes the immunity repressor CB. We have characterized a second locus, immA, in which clear plaque mutations were mapped, and found that it encodes an anti-immunity system involved in the choice between the lytic and the lysogenic cycle. Three open reading frames at the immA locus encode an inhibitor of cell division (icd ), an antirepressor (antA) and a gene that may play an ancillary role in anti-immunity (antB ). These genes may be transcribed from two promoters: the upstream promoter Pa is repressed by the immunity repressor CB, whereas the downstream promoter Pb is constitutive. Full repression of the anti-immunity system is achieved by premature transcription termination elicited by a small RNA (CA RNA) produced by processing of the leader transcript of the anti-immunity operon. The N15 anti-immunity system is structurally and functionally similar to the anti-immunity system of bacteriophage P1 and to the immunity system of satellite phage P4.

Use of a linear multicopy vector based on the mini-replicon of temperate coliphage N15 for cloning DNA with abnormal secondary structures

A new cloning vector pN15L is described. It is a linear 13.8 kb plasmid based on the coliphage N15 mini-replicon. The vector capacity exceeds 50 kb and the copy number is 250 per Escherichia coli chromosome. We show that some artificial and natural palindromes and approximately 5% of human DNA Bgl II fragments can be cloned effectively in linear vector pN15L, whereas they either sharply reduce the copy number of circular vector pUC19 or cannot be cloned at all. We conclude that pN15L may be usefully employed to clone large imperfect palindromes and some abnormal sequences of human DNA.

[COS-region of temperate coliphage N15]

The cohesive termini including the cos region (altogether 414 bp) of the DNA of the temperate coliphage N15 are sequenced. The termini are complementary 12-nucleotide single-stranded 5'-extended DNAs. The sequence of the left terminus is 5'-GGGCGGCGTCCG-3', that of the right 5'CGGACGCCGCCC-3'. Ten nucleotides of the N15 termini are identical to those of phage lambda. The N15 and lambda sequences are notably homologous only within the 50 bp region from the left and right ends. Phage N15 has a region with the nucleotide sequence identical to the R4 site of phage lambda, presumably reacting with terminase. This region is situated in the same site with regard to the cohesive sequence as in phage lambda. The cos region of N15 has no sequences similar to R1, R2, and R3 of lambda. N15 has a sequence similar to IHF of phage lambda, but in N15 this sequence is located near the right but not left (as in phage lambda) terminus. Computer analysis revealed palindromes and repeats within 450 bp of N15, including the cohesive termini.

[Cloning of large imperfect palindromes in circular and linear vectors]

Data on comparative analysis of cloning of large imperfect artificial palindromes and one natural palindrome in the circular pUC19 and linear pN15L vectors, constructed on the basis of temperate N15 bacteriophage minireplicon are presented. The artificial palindromes consisted of the two head-to-head oriented 5:5-kb lambda bacteriophage DNA fragments interrupted by a short sequence of varied size. Natural palindrome was represented by the 12.5-kb BamHI fragment of Tetrahymena pyriformis ribosomal genes cluster. Integration of some artificial palindromes and a natural palindrome into a circular vector resulted in a considerable decrease of its copy number. This was assumed to result from cruciform formation mediated by supercoiling of a circular vector DNA. Thus, a linear is vector preferable in cloning of inverted repeated DNA sequences.

[Supercopy plasmid based on the replicon from the temperate N15 bacteriophage]

Mini-plasmids, based on the N15 temperate bacteriophage replicon, are described. One of these, N15-203 linear 13.8 kb plasmid, has anomalously high copy number--more than 250 per one bacterial chromosome and the amount of plasmid DNA comprises about half of the total DNA of a cell. This property of N15-203 plasmid is realized only in the strain lysogenic for a N15 phage and is lost for the circular deletion versions of N15-203. The efficiency of transformation of E. coli C (N15) strain is essentially the same for N15-203 and pUC4K plasmids. Insertion of foreign DNA with a size up to 20 kb into BgIII cloning site of N15-203 plasmid does not decrease significantly efficiency of transformation calculated per number of DNA molecules and the total amount of plasmid DNA in a cell. N15-203 plasmid may be used as a vector for molecular cloning of relatively large DNA fragments, and in those biotechnology processes when productivity depends on a vector's copy number.