Patent Grant
9394561
This invention is related to biochemistry, more specifically to polypeptides, nucleic acid molecules and processes for producing cyclic peptides.
Cyclic peptides (CPs) have commercial value as drugs, antimicrobial compounds and antigens in vaccines, but they can be difficult and expensive to produce. Also, the ability to make cyclic peptides of any size and sequence is commercially desirable both for screening of thousands of CPs for biological activity and for the production of specific valuable cyclic peptides.
According to the present knowledge, the so-called homodetic cyclic peptides or homocylopetides, which have a ring composed of amino acids linked by peptide bonds, can be produced by: extraction from natural sources, especially plants, fungi and microbes (Pomilio 2006; Tan 2006; Craik 2007; Cascales 2010; Morita 2010); chemical synthesis (White 2011; Lambert 2001; Davies 2003); cyclization of linear peptide precursors using isolated enzymes (Bolscher 2011; Katoh 2011; Grunewald 2006) including Staphylococcus aureus sortase A (Wu 2011), the Prochloron didemni patG gene product (McIntosh 2010) and trypsin (Thongyoo 2008); and, genetic engineering of various organisms including bacteria and plants, using genes encoding split inteins (Young 2011) and other inteins variants (Katoh 2011; Camarero 2011; Austin 2009), proteases and their homologues and/or cyclic peptide precursors (Katoh 2011; Condie 2011; Donia 2008; Tang 2011; Covello 2010; Schmidt 2010; Schmidt 2007) and non-ribosomal peptide synthetases (Kohli 2001).
Particularly relevant is the production of cyclic peptides based on the process which occurs in plants of the Caryophyllaceae family. It has been shown that in this family, precursor peptides are encoded by DNA (Condie 2011). When a DNA fragment encoding precursors is experimentally expressed in genetically transformed roots of Saponaria vaccaria, for example, a corresponding cyclic peptide is produced in the roots. Similarly, when a chemically synthesized precursor peptide is incubated with extracts of Saponaria vaccaria, a corresponding cyclic peptide is produced.
Also relevant is the use of purified enzymes, especially from recombinant microbes, for in vitro peptide cyclization. Generally these involve the use of chemically synthesized linear peptides which are incubated with a purified enzyme, such as sortase A or the patG gene product, capable of catalyzing the formation of a cyclic peptide from part of the linear peptide.
Existing methods have one or more drawbacks. Extraction from natural sources, especially plants, fungi and microbes is limited by the natural variation and abundance of cyclic peptides from these sources. Depending on the size and composition of the desired CP product, chemical synthesis can be complicated and expensive. Peptide cyclization by sortase A is limited to CP products which include a sorting sequence and usually one or two glycine residues. Production of desired CP product using the split intein method varies widely depending on the sequence. Use of inteins variants usually requires the inclusion of a cysteine in the cyclic product. In vivo peptide cyclization by sortase A is limited to CP products which include a sorting sequence and usually one or two glycine residues. Use of non-ribosomal peptide synthetases generally requires a substrate with a C-terminal thioester moiety.
There remains a need for alternative methods of producing cyclic peptides that overcomes one or more of the drawbacks of the prior art.
In an embodiment, there is provided an isolated nucleic acid molecule comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence as set forth in SEQ ID NO: 1, a full length complement thereof or a codon degenerate nucleotide sequence thereof.
In an embodiment, there is provided an isolated polypeptide comprising: an amino acid sequence having at least 80% sequence identity to the amino acid sequence as set forth in SEQ ID NO: 2; or, a conservatively substituted amino acid sequence of the amino acid sequence as set forth in SEQ ID NO: 2.
Nucleic acid molecule and polypeptides of the present invention are preferably from Caryophyllaceae family of plants, or are artificial sequences created therefrom by mutation, for example. Genera in the Caryophyllaceae family include, for example, Acanthophyllum, Achyronychia, Agrostemma, Allochrusa, Alsinidendron, Ankyropetalum, Arenaria, Bolanthus, Bolbosaponaria, Brachystemma, Bufonia, Cardionema, Cerastium, Cerdia, Colobanthus, Cometes, Corrigiola, Cucubalus, Cyathophylla, Dianthus, Diaphanoptera, Dicheranthus, Drymaria, Drypis, Eremogone, Geocarpon, Gymnocarpos, Gypsophila, Habrosia, Haya, Herniaria, Holosteum, Honckenya, Illecebrum, Kabulia, Krauseola, Kuhitangia, Lepyrodiclis, Lochia, Loeflingia, Lychnis, Melandrium, Mesostemma, Microphyes, Minuartia, Moehringia, Moenchia, Myosoton, Ochotonophila, Ortegia, Paronychia, Pentastemonodiscus, Petrocoptis, Petrorhagia, Philippiella, Phrynella, Pinosia, Pirinia, Pleioneura, Plettkia, Pollichia, Polycarpaea, Polycarpon, Polytepalum, Pseudostellaria, Pteranthus, Pycnophyllopsis, Pycnophyllum, Reicheella, Sagina, Sanctambrosia, Saponaria, Schiedea, Scleranthopsis, Scleranthus, Sclerocephalus, Scopulophila, Selleola, Silene, Spergula, Spergularia, Sphaerocoma, Stellaria, Stipulicida, Thurya, Thylacospermum, Uebelinia, Vaccaria, Velezia, Wilhelmsia and Xerotia.
In an embodiment, there is provided a nucleic acid construct comprising a nucleic acid molecule of the present invention operatively linked to one or more nucleotide sequences for aiding in transformation or transfection of a cell with the construct. The embodiment also relates to a construct comprising an isolated nucleic acid molecule of the present invention operably linked to suitable regulatory sequences. The construct may be a chimeric gene construct.
In an embodiment, there is provided a host cell comprising a construct or an isolated nucleic acid molecule of the present invention. The host cell may be eukaryotic, such as a yeast or a plant cell, or prokaryotic, such as a bacterial cell. This embodiment also relates to a virus comprising a chimeric gene construct or an isolated nucleic acid molecule of the present invention.
In an embodiment, there is provided a process for producing a host cell comprising a construct or an isolated nucleic acid molecule of the present invention, the process comprising transforming or transfecting a compatible host cell with a chimeric gene construct or an isolated nucleic acid molecule of the present invention.
In an embodiment, there is provided a process of producing a cyclic peptide, the process comprising contacting a suitable linear peptide precursor of the cyclic peptide with an isolated polypeptide comprising an amino acid sequence having at least 75% sequence identity to the amino acid sequence as set forth in SEQ ID NO: 2 or a conservatively substituted amino acid sequence of the amino acid sequence as set forth in SEQ ID NO: 2 to produce the cyclic peptide from the linear peptide precursor. A suitable linear peptide precursor is a linear peptide that is capable as acting a substrate for the polypeptide of the present invention, where the action of the polypeptide on the linear peptide produces the cyclic peptide. The process may be performed in vitro, or in vivo in a host cell or organism transformed or transfected with a construct or nucleic acid molecule of the present invention. The linear peptide precursor may be produced chemically or through recombinant organisms.
The present invention permits production of a wide range of cyclic peptides which find use as drugs, antimicrobial compounds, vaccine antigens or nanotube related technologies. The present invention may also be used to generate large libraries of cyclic peptides for screening to identify cyclic peptides of commercial interest.
In another embodiment, there is provided a method of reducing cyclopeptide content in a host cell, tissue or plant comprising: reducing expression in the cell, tissue or plant of a nucleic acid molecule comprising a nucleotide sequence having at least 80% sequence identity to the nucleotide sequence as set forth in SEQ ID NO: 1, compared to expression of the nucleotide sequence in the cell, tissue or plant before expression was reduced.
Further features of the invention will be described or will become apparent in the course of the following detailed description.
In order that the invention may be more clearly understood, embodiments thereof will now be described in detail by way of example, with reference to the accompanying drawings, in which:
In order to facilitate review of the various embodiments of the disclosure, the following explanations of specific terms are provided:
Complementary nucleotide sequence: “Complementary nucleotide sequence” of a sequence is understood as meaning any DNA whose nucleotides are complementary to those of sequence of the disclosure, and whose orientation is reversed (antiparallel sequence).
Degree or percentage of sequence homology: The term “degree or percentage of sequence homology” refers to degree or percentage of sequence identity between two sequences after optimal alignment. Percentage of sequence identity (or degree or identity) is determined by comparing two optimally aligned sequences over a comparison window, where the portion of the peptide or polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical amino-acid residue or nucleic acid base occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.
Isolated: As will be appreciated by one of skill in the art, “isolated” refers to polypeptides or nucleic acids that have been “isolated” from their native environment.
Nucleotide, polynucleotide, or nucleic acid sequence: “Nucleotide, polynucleotide, or nucleic acid sequence” will be understood as meaning both a double-stranded or single-stranded DNA in the monomeric and dimeric (so-called in tandem) forms and the transcription products of said DNAs.
Sequence identity: Two amino-acid or nucleotide sequences are said to be “identical” if the sequence of amino-acids or nucleotide residues in the two sequences is the same when aligned for maximum correspondence as described below. Sequence comparisons between two (or more) peptides or polynucleotides are typically performed by comparing sequences of two optimally aligned sequences over a segment or “comparison window” to identify and compare local regions of sequence similarity. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman (Smith 1981), by the homology alignment algorithm of Neddleman and Wunsch (Neddleman 1970), by the search for similarity method of Pearson and Lipman (Pearson 1988), by computerized implementation of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by visual inspection. Isolated and/or purified sequences of the present invention or used in the present invention may have a percentage identity with the bases of a nucleotide sequence, or the amino acids of a polypeptide sequence, of at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, or 99.7%. When used in a process of producing a cyclic peptide, the sequences may have a percentage identity with the bases of a nucleotide sequence, or the amino acids of a polypeptide sequence, of at least about 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, or 99.7%. These percentages are purely statistical, and it is possible to distribute the differences between two nucleotide or amino acid sequences at random and over the whole of their length.
It will be appreciated that this disclosure embraces the degeneracy of codon usage as would be understood by one of ordinary skill in the art and as illustrated in Table 1.
Furthermore, it will be understood by one skilled in the art that conservative substitutions may be made in the amino acid sequence of a polypeptide without disrupting the structure or function of the polypeptide. Conservative substitutions are accomplished by the skilled artisan by substituting amino acids with similar hydrophobicity, polarity, and R-chain length for one another. Additionally, by comparing aligned sequences of homologous proteins from different species, conservative substitutions may be identified by locating amino acid residues that have been mutated between species without altering the basic functions of the encoded proteins. Table 2 provides an exemplary list of conservative substitutions.
The definition of sequence identity given above is the definition that would be used by one of skill in the art. The definition by itself does not need the help of any algorithm, said algorithms being helpful only to achieve the optimal alignments of sequences, rather than the calculation of sequence identity. From the definition given above, it follows that there is a well defined and only one value for the sequence identity between two compared sequences which value corresponds to the value obtained for the best or optimal alignment. In the BLAST N or BLAST P “BLAST 2 sequence”, software which is available in the web site http://www.ncbi.nlm.nih.gov/gorf/bl2.html, and habitually used by the inventors and in general by the skilled man for comparing and determining the identity between two sequences, gap cost which depends on the sequence length to be compared is directly selected by the software (i.e. 11.2 for substitution matrix BLOSUM-62 for length>85).
Expression
Nucleic acid molecules of the present invention can be expressed in alternate plant hosts to impart characteristics of improved agronomic performance via recombinant means. The methods to construct expression vectors and to transform and express foreign genes in plant and plant cells are well known in the art.
Such heterologous expression can also be conducted in microorganisms, such as in bacteria (e.g. E. coli), yeast (e.g. S. cerevisiae) and in fungi, which can this serve as host for the recombinant expression of the nucleic acid molecules and for the production and isolation of cyclopeptides produced therefrom.
Additionally, it is evident that the nucleic acid molecules can be used in the construction of expression vectors for heterologous expression in diverse host cells and organisms by conventional techniques. These methods, which can be used in the invention, have been described elsewhere (Potrykus 1991; Vasil 1994; Walden 1995; Songstad 1995), and are well known to persons skilled in the art. As known in the art, there are a number of ways by which genes and gene constructs can be introduced into plants and other organisms and a combination of transformation/transfection and tissue culture techniques have been successfully integrated into effective strategies for creating transgenic organisms. For example, one skilled in the art will certainly be aware that, in addition to Agrobacterium-mediated transformation of Arabidopsis by vacuum infiltration (Bechtold 1993) or wound inoculation (Katavic 1994), it is equally possible to transform other plant species, using Agrobacterium Ti-plasmid mediated transformation (e.g., hypocotyl (DeBlock 1989) or cotyledonary petiole (Moloney 1989) wound infection), particle bombardment/biolistic methods (Sanford 1987; Nehra 1994; Becker 1994) or polyethylene glycol-assisted, protoplast transformation (Rhodes 1988; Shimamoto 1989) methods.
As will also be apparent to persons skilled in the art, and as described elsewhere (Meyer 1995; Datla 1997), it is possible to utilize promoters to direct any intended regulation of transgene expression using constitutive promoters (e.g., those based on CaMV35S), or by using promoters which can target gene expression to particular cells, tissues (e.g., napin promoter for expression of transgenes in developing seed cotyledons), organs (e.g., roots), to a particular developmental stage, or in response to a particular external stimulus (e.g., heat shock). Promoters for use herein may be inducible, constitutive, or tissue-specific or cell specific or have various combinations of such characteristics. Useful promoters include, but are not limited to constitutive promoters such as carnation etched ring virus (CERV), cauliflower mosaic virus (CaMV) 35S promoter, or more particularly the double enhanced cauliflower mosaic virus promoter, comprising two CaMV 35S promoters in tandem (referred to as a “Double 35S” promoter). Meristem specific promoters include, for example, STM, BP, WUS, CLV gene promoters. Seed specific promoters include, for example, the napin promoter. Other cell and tissue specific promoters are well known in the art.
Promoter and termination regulatory regions that will be functional in the host cell may be heterologous (that is, not naturally occurring) or homologous (derived from the host species) to the cell and the gene. Suitable promoters which may be used are described above. The termination regulatory region may be derived from the 3′ region of the gene from which the promoter was obtained or from another gene. Suitable termination regions which may be used are well known in the art and include Agrobacterium tumefaciens nopaline synthase terminator (Tnos), A. tumefaciens mannopine synthase terminator (Tmas) and the CaMV 35S terminator (T353). Particularly preferred termination regions for use herein include the pea ribulose bisphosphate carboxylase small subunit termination region (TrbcS) or the Tnos termination region. Such gene constructs may suitably be screened for activity by transformation/transfection into a host via Agrobacterium and screening for the desired activity using known techniques.
Preferably, a nucleic acid molecule construct for use herein is comprised within a vector, most suitably an expression vector adapted for expression in an appropriate cell. It will be appreciated that any vector which is capable of producing an organism comprising the introduced nucleic acid sequence will be sufficient. Suitable vectors are well known to those skilled in the art and are described in general technical references. Particularly suitable vectors include the Ti plasmid vectors. After transformation/transfection of the cells or organism, those cells or organisms into which the desired nucleic acid molecule has been incorporated may be selected by such methods as antibiotic resistance, herbicide resistance, tolerance to amino-acid analogues or using phenotypic markers. Various assays may be used to determine whether the cell shows an increase in gene expression, for example, Northern blotting or quantitative reverse transcriptase PCR (RT-PCR). Whole transgenic organisms may be regenerated from the transformed/transfected cell by conventional methods. When the organism is a plant, such plants produce seeds containing the genes for the introduced trait and can be grown to produce plants that will produce the selected phenotype.
Silencing
Silencing may be accomplished in a number of ways generally known in the art, for example, RNA interference (RNAi) techniques, artificial microRNA techniques, virus-induced gene silencing (VIGS) techniques, antisense techniques, sense co-suppression techniques and targeted mutagenesis techniques.
RNAi techniques involve stable transformation using RNA interference (RNAi) plasmid constructs (Helliwell 2005). Such plasmids are composed of a fragment of the target gene to be silenced in an inverted repeat structure. The inverted repeats are separated by a spacer, often an intron. The RNAi construct driven by a suitable promoter, for example, the Cauliflower mosaic virus (CaMV) 35S promoter, is integrated into the plant genome and subsequent transcription of the transgene leads to an RNA molecule that folds back on itself to form a double-stranded hairpin RNA. This double-stranded RNA structure is recognized by the plant and cut into small RNAs (about 21 nucleotides long) called small interfering RNAs (siRNAs). siRNAs associate with a protein complex (RISC) which goes on to direct degradation of the mRNA for the target gene.
Artificial microRNA (amiRNA) techniques exploit the microRNA (miRNA) pathway that functions to silence endogenous genes in plants and other eukaryotes (Schwab 2006; Alvarez 2006). In this method, 21 nucleotide long fragments of the gene to be silenced are introduced into a pre-miRNA gene to form a pre-amiRNA construct. The pre-miRNA construct is transferred into the plant genome using transformation methods apparent to one skilled in the art. After transcription of the pre-amiRNA, processing yields amiRNAs that target genes which share nucleotide identity with the 21 nucleotide amiRNA sequence.
In RNAi silencing techniques, two factors can influence the choice of length of the fragment. The shorter the fragment the less frequently effective silencing will be achieved, but very long hairpins increase the chance of recombination in bacterial host strains. The effectiveness of silencing also appears to be gene dependent and could reflect accessibility of target mRNA or the relative abundances of the target mRNA and the hpRNA in cells in which the gene is active. A fragment length of between 100 and 800 bp, preferably between 300 and 600 bp, is generally suitable to maximize the efficiency of silencing obtained. The other consideration is the part of the gene to be targeted. 5′ UTR, coding region, and 3′ UTR fragments can be used with equally good results. As the mechanism of silencing depends on sequence homology there is potential for cross-silencing of related mRNA sequences. Where this is not desirable a region with low sequence similarity to other sequences, such as a 5′ or 3′ UTR, should be chosen. The rule for avoiding cross-homology silencing appears to be to use sequences that do not have blocks of sequence identity of over 20 bases between the construct and the non-target gene sequences. Many of these same principles apply to selection of target regions for designing amiRNAs.
Virus-induced gene silencing (VIGS) techniques are a variation of RNAi techniques that exploits the endogenous antiviral defenses of plants. Infection of plants with recombinant VIGS viruses containing fragments of host DNA leads to post-transcriptional gene silencing for the target gene. In one embodiment, a tobacco rattle virus (TRV) based VIGS system can be used.
Antisense techniques involve introducing into a plant an antisense oligonucleotide that will bind to the messenger RNA (mRNA) produced by the gene of interest. The “antisense” oligonucleotide has a base sequence complementary to the gene's messenger RNA (mRNA), which is called the “sense” sequence. Activity of the sense segment of the mRNA is blocked by the anti-sense mRNA segment, thereby effectively inactivating gene expression. Application of antisense to gene silencing in plants is described in more detail by Stam 2000.
Sense co-suppression techniques involve introducing a highly expressed sense transgene into a plant resulting in reduced expression of both the transgene and the endogenous gene (Depicker 1997). The effect depends on sequence identity between transgene and endogenous gene.
Targeted mutagenesis techniques, for example TILLING (Targeting Induced Local Lesions IN Genomes) and “delete-a-gene” using fast-neutron bombardment, may be used to knockout gene function in a plant (Henikoff 2004; Li 2001). TILLING involves treating seeds or individual cells with a mutagen to cause point mutations that are then discovered in genes of interest using a sensitive method for single-nucleotide mutation detection. Detection of desired mutations (e.g. mutations resulting in the inactivation of the gene product of interest) may be accomplished, for example, by PCR methods. For example, oligonucleotide primers derived from the gene of interest may be prepared and PCR may be used to amplify regions of the gene of interest from plants in the mutagenized population. Amplified mutant genes may be annealed to wild-type genes to find mismatches between the mutant genes and wild-type genes. Detected differences may be traced back to the plants which had the mutant gene thereby revealing which mutagenized plants will have the desired expression (e.g. silencing of the gene of interest). These plants may then be selectively bred to produce a population having the desired expression. TILLING can provide an allelic series that includes missense and knockout mutations, which exhibit reduced expression of the targeted gene. TILLING is touted as a possible approach to gene knockout that does not involve introduction of transgenes, and therefore may be more acceptable to consumers. Fast-neutron bombardment induces mutations, i.e. deletions, in plant genomes that can also be detected using PCR in a manner similar to TILLING.
Silencing of genes that encode the enzymes of the present invention may be useful to reduce levels of undesirable cyclopeptides in plants, and to facilitate production of a single cyclopeptide so as to simplify extraction/purification.
Previously it was shown that in the Caryophyllaceae family, cyclic peptides are produced from linear peptides which are DNA-encoded.
However, why cyclic peptides are produced from such linear precursor peptides remained unknown. In the present invention, it has now been shown that the production of cyclic peptides from such linear precursors is accomplished enzymatically. As a result of the present invention, it can now be hypothesized that the pathway from presegetalin A1 to segetalin A involves initial cleavage of presegetalin A1 after position 13, giving rise to hitherto unknown intermediate linear precursors presegetalin A1[1,13] (SEQ ID NO: 16) and presegetalin A1[14,32] (SEQ ID NO: 15), as shown in
In general, for the enzymatic production of cyclic peptides using an enzyme of the present invention, suitable immediate linear peptide precursors comprise the amino acid sequence that will form the cyclic peptide at one terminus of the linear peptide precursor, preferably the N-terminus, and a flanking region that is cleaved away from the cyclic peptide-forming amino acid sequence during formation of the cyclic peptide.
Chemicals
Presegetalin A1 (SEQ ID NO: 3, Mr=3400.30; purity≧75%) and presegetalin A1[14,32] (SEQ ID NO: 15, Mr=1984.05; purity>75%) were chemically synthesized at the Sheldon Biotechnology Centre, McGill University. The presegetalin A1 was further purified by a standard peptide HPLC fractionation on a C18 column using a water to acetonitrile gradient (with TFA as modifier). Segetalin A (SEQ ID NO: 14) was isolated from S. vaccaria seed by the method of Morita (Morita 1994).
Plant Material
Saponaria vaccaria ‘White Beauty’ seeds were obtained from CN Seeds Ltd (United Kingdom). Plants were grown under a daily regime of 16 h light (150 μEinstein m−2 s−1) at 24° C. and 8 h dark at 20° C. Stage 2 developing seeds were harvested according to the following scheme: Stage 1, seed white, pod green; Stage 2, seed tan; Stage 3, seed copper, pod partially dessicated; Stage 4, seed dark brown, pod dessicated.
In Vitro Processing of Presegetalin A1
Stage 2 developing seeds from S. vaccaria (var. White Beauty) were homogenized manually with a plastic pestle in 1.5 mL low protein binding microcentrifuge tubes. One gram of seeds was ground for 2 min in 4×250 μL 20 mM Tris buffer (pH 8) on ice followed by centrifugation at 13,000×g for 5 min. The supernatant was removed and another 250 μL buffer was added and the grinding and centrifugation was repeated. The supernatant fractions were pooled and this crude extract was used for enzyme assays. The crude extract protein was measured using Bradford reagent with BSA as a calibration standard (BioRad). The in vitro assay contained 20 mM Tris, 100 mM NaCl, 2 mM DTT, 0.2 mg BSA and 25 μg/mL presegetalin A1 and was initiated by the addition of crude extract, equivalent to 4.0 μg protein, in a total reaction volume of 100 μL. Unless otherwise stated, the assay was performed at pH 8.5. The assays were incubated at 30° C. for up to 5 h and stopped by placing reactions in dry ice. The assays were lyophilized, re-suspended in methanol, evaporated and re-suspended in 50:50 v/v methanol/water for LC/MS analysis.
Ion trap ESI+ LC/MS analysis was used to detect production of segetalin A using an Agilent 6320 Ion Trap LC/MS system under default Smart Parameter settings. The analyzer and ion optics were adjusted to achieve proper resolution (Agilent Installation Guide #G2440-90105) using the ESI Tuning Mix (Agilent #G2431A). The mass spectrometer scanned in the m/z range of 50 to 2200 at 8100 mass units/s with an expected peak width of ≦0.35 mass units. For automated MS/MS, the trap isolation width was 4 atomic mass units. The associated Agilent 1200 LC was fitted with a Zorbax™ 300 EXTEND-C18 column (150×2.1 mm, 3.5 μm particle size) maintained at 35° C. The binary solvent system consisted of 90:10 v/v water/acetonitrile containing 0.1% formic acid and 0.1% ammonium formate (solvent A) and 10:90 v/v water/acetonitrile containing 0.1% formic acid and 0.1% ammonium formate (solvent B). The separation gradient was 90:10 A/B to 50:50 A/B in 3 mL over 20 min. The detection of segetalin A in assay samples is described previously (Condie 2011).
Fractionation of S. vaccaria Developing Seed Extracts
In an effort to elucidate the enzymes and possible peptide intermediates which could be involved in peptide cyclization in developing seeds of Saponaria vaccaria, extracts of the seeds were subjected to fractionation by liquid chromatography and subsequent biochemical analysis. Two mg of total soluble protein from stage 2 developing seed (var. White Beauty) was fractionated (1 mL fraction volume) on a MonoQ 5/50 GL ion exchange column (GE Healthcare, Life Sciences, Mississauga, Canada) with 20 mM Tris pH 8.0 as the buffer and a gradient of 0 to 0.8 M NaCl over a volume of 10 mL using an Agilent 1100 HPLC equipped with an auto injector, diode array detector and fraction collector. These fractions were assayed for loss of substrate and the production of segetalin A and other possible products, using presegetalin A1 as a substrate (see above). HPLC analysis of fractions showed significant loss of presegetalin A1 in fractions 4 through 9 (peaking in fractions 5 and 6) and production of segetalin A in fraction 4.
In an effort to identify intermediates formed during precursor processing, assay samples were analyzed by MALDI-TOF MS. Samples were purified by adsorption onto and elution from C18 Empore™ High Performance Disk material (3M, Minneapolis, Minn., USA) using the “Stage tip” method (Rappsilber 2003). Stage tips were prepared by removing the beveled tip from a 20 gauge syringe needle with a tubing cutter. Empore™ disk material was then cut, cookie cutter style, with this needle and packed into the tip of a 10 μL pipette tip with a piece of fused silica tubing. Methanol (10 μL) was applied to the tip and expelled slowly with a 1.25 mL syringe. Aqueous trifluoroacetic acid (TFA; 0.1%) was then passed through the tip, followed by assay sample (20 μL). The disk material was washed with 20 μl 0.1% TFA and peptides were then eluted with 20 μL acetonitrile:aqueous 0.1% TFA.
Analysis of the peptides was carried out using an AB Sciex™ 4800 Plus MALDI TOF-TOF™ Analyzer. The mass spectrometer was operated in positive ion reflectron mode scanning from m/z values of 500 to 4000. The default calibration was updated with a standard mixture of peptides containing des-Arg1 bradykinin (m/z 904.468), Gu1 fibrinopeptide B (m/z 1570.677), and three ACTH fragments corresponding to amino acids 1-17 (m/z 2093.087), 18-39 (m/z 2465.199), and 7-38 (m/z 3657.929). All samples and calibrants (0.5 μL) were mixed on the MALDI plate with the matrix α-cyano-4-hydroxycinnamic acid (0.5 μL). Data were collected and averaged from 800 laser desorption events. Monoisotopic mass lists were generated with Data Explorer™ (Applied Biosystems) and copied into the Biolynx™ program in Masslynx™ 4.0 (Waters). Matches to subsequences of presegetalin A1 were investigated using the Find Mass program with an allowed mass deviation of 0.5 Da. Masses within 0.2 Da were considered to be matching.
The MALDI-TOF MS analysis for fraction 8 showed prominent peaks corresponding to peptide masses of 1302.7, 1433.8 and 1984.0 which, in turn, correspond to linear peptides with the sequences MSPILAHDVVKPQ (SEQ ID NO: 16), SPILAHDVVKPQ (SEQ ID NO: 17) and GVPVWAFQAKDVENASAPV (SEQ ID NO: 15), respectively. This suggests that cleavage of the QG peptide bond is an important reaction in the biosynthesis of segetalin A. Taken together, the data are consistent with a peptide with the sequence GVPVWAFQAKDVENASAPV (SEQ ID NO: 15) being an intermediate in segetalin A biosynthesis. As well, the data are consistent with the presence of exopeptidase activity. Thus, the pathway from presegetalin A1 to segetalin A shown in
In Vitro Assay to Test PCY1 Activity
The gene corresponding to S. vaccaria PCY1 was cloned and expressed in E. coli with a His-tag. HisPur Cobalt Resin™ (Thermo Scientific) was used for purification of recombinant PCY1. The purified PCY1 was quantified using BCA method (Pierce; http://http://www.piercenet.com/) with BSA as a calibration standard. The in vitro assay contained 20 mM Tris buffer (pH 8.5), 100 mM NaCl, 5 mM DTT, 0.2 mg BSA, and 1.5 μg of substrates (wild type and mutant presegetalins, procured from Bio Basic Inc with >90% purity) and was initiated by the addition of 0.3 μg of PCY1, in a total reaction volume of 100 μl. The assay was incubated at 30° C. for up to 1 h and stopped by placing reactions in dry ice. The assays were lyophilized, re-suspended in methanol, evaporated and re-suspended in 50:50 v/v methanol/water for LC/MS analysis.
LC/MS Analysis of Assays
Ion trap ESI+ LC/MS/MS analysis was used to detect production of cyclic peptides using an Agilent 6320 Ion Trap LC/MS system under default Smart Parameter settings. The analyzer and ion optics were adjusted to achieve proper resolution (Agilent Installation Guide #G2440-90105) using the ESI Tuning Mix (Agilent #G2431A). The mass spectrometer scanned from 50 to 2200 mass units at 8100 mass units sec−1 with an expected peak width of 0.35 atomic mass units. For auto MS/MS, the trap isolation width was 4 atomic mass units. The associated Agilent 1200 LC was fitted with a Zorbax 300 EXTEND-C18 column (150×2.1 mm, 3.5 μm particle size) maintained at 35° C. The binary solvent system consisted of 90:10 v/v water/acetonitrile containing 0.1% formic acid and 0.1% ammonium formate (solvent A) and 10:90 v/v water/acetonitrile containing 0.1% formic acid and 0.1% ammonium formate (solvent B). The separation gradient was 90:10 A/B to 50:50 A/B in 3 ml over 20 min.
The scheme in
With a view towards complete characterization of the enzyme, its purification from plant material was attempted. The enzyme was partially purified from the developing seed extracts using ion-exchange chromatography, hydrophobic interaction chromatography and size exclusion chromatography.
S. vaccaria Developing Seed Extract
All purification steps were performed on ice or at 4° C. Eight grams of frozen Stage 2 embryos were divided into twenty 1.5 mL Eppendorf™ tubes and ground with a small pestle in 500 μL aliquots of 20 mM Tris-HCl (pH 8.0). The resulting slurries were centrifuged twice to fully remove sediment and floating debris from supernatant for 10 min at 12,000 g, and the pooled supernatant of 17 mL was passed through a 25 mm cellulose acetate membrane syringe filter (0.2 μm pore size; VWR International, Mississauga, Canada) followed by three sequential chromatographic separations, as detailed below.
Chromatography
All chromatographic elution was monitored spectrophotometrically at 280 nm. Three separate applications of five mL each of the filtrate (see above) were applied to an anion exchange column (Mono Q 10/100, GE Healthcare Life Sciences, Mississauga, Canada) connected to an Agilent 1100 series HPLC. The column was held at 4° C. and pre-equilibrated with 20 mM Tris-HCl (pH 8.0). The column was eluted with 60 mL of a linear gradient of NaCl (0-1 M) in 20 mM Tris-HCl (pH 8.0) at a flow rate of 1 mL/min. One mL fractions were collected, desalted with Sephadex™ G-25 M PD-10 columns (GE Healthcare Life Sciences, Mississauga, Canada), concentrated in Amicon™ Ultra centrifugal filters (Ultracel™-30K cellulose 30 MWCO; Millipore, Bellerica, Mass., USA) and assayed for the production of segetalin A in the presence of presegetalin A1[14,32]. The active fractions were combined and applied to a hydrophobic interaction perfusion chromatography column with PerSeptive POROS™ 20 HP2 (Bio-Rad Laboratories (Canada) Ltd, Mississauga, Canada) pre-equilibrated with 3 M ammonium sulfate in 20 mM Tris-HCl (pH 8.0) which was eluted with a decreasing linear gradient (3-0 M) of 60 mL ammonium sulfate at a flow rate of 4 mL/min. One mL fractions were collected over 15 min and desalted and concentrated by ultracentrifugation with Amicon™ Ultra centrifugal filters (Ultracel™-30K cellulose 30 MWCO, Millipore, Bellerica, Mass., USA). The resulting fractions were assayed for enzyme activity (segetalin A production). Active fractions were combined and concentrated to 100 μL with Amicon™ Ultra centrifugal 30 MWCO filters. The resulting sample was then applied to a Superose™ 6 10/300 Gel Filtration column (GE Healthcare Life Sciences, Mississauga, Canada) which had been pre-equilibrated with 20 mM Tris-HCl (pH 8.0). Proteins were eluted with 20 mM Tris-HCl (pH 8.0) at a flow rate of 0.2 mL/min for 145 min. One mL fractions were collected, concentrated with Amicon™ Ultracel-10K membrane centrifugal filter units and assayed for enzyme activity. The retention times of standard proteins (thyroglobulin (Mr=669,000), ferritin (Mr=440,000), catalase (Mr=232,000), aldolase (Mr=158,000), BSA (Mr=67,000), ovalbumin (Mr=43,000), chymotrypsinogen (Mr=25,000) and ribonuclease A (Mr=14,000); GE Healthcare Life Sciences, Mississauga, Canada) were measured in a separate chromatography experiment under identical conditions. The size exclusion chromatography indicated that the relative molecular mass of the enzyme was approximately 90,000 (data not shown).
SDS Polyacrylamide Gel Electrophoresis
Active fractions from the various stages of chromatography were mixed 1:1 with SDS PAGE Laemmli sample buffer (200 mM Tris-HCl, pH 6.8, 4% SDS, 0.2% bromophenol blue, 200 mM dithiothreitol, 40% glycerol) and heated at 99° C. for 5 min. The samples were subjected to SDS-PAGE under denaturing conditions in Electrophoresis Buffer (25 mM Tris-HCl, pH 7.5, 250 mM glycine, 0.1% SDS) for 4 h at 30 mA using a 10% Ready GeI™ pre-cast polyacrylamide mini-gel and a Mini-PROTEAN™ II (Bio-Rad Laboratories (Canada) Ltd, Mississauga Canada) apparatus. Precision Plus Protein™ molecular weight standards (Bio-Rad) were loaded on the same gel. The gel was stained with Oriole™ Fluorescent Gel Stain (Bio-Rad Laboratories (Canada) Ltd, Mississauga Canada) for 15 h. Protein bands were visualized by UV illumination (see
Protein Analysis
Gel bands derived from the active fraction of the final chromatography step were subjected to proteolysis and LC/MS as described below. Iodoacetamide (IAA) and dithiothreitol (DTT) were purchased from Bio-Rad (Hercules, Calif., USA); trifluoroacetic acid, ammonium bicarbonate and HPLC grade acetonitrile were purchased from Fisher Scientific (Fair Lawn, N.J., USA). Formic acid was from Acros (New Jersey, USA). Distilled water was purified using a MilliQ™ Element water purification system (Millipore, Billerica, Mass. USA). Sequencing grade modified trypsin (Trypsin Gold) was purchased from Promega (Madison, Wis., USA).
In-Gel Digestion Procedure
Gel bands excised from SDS-PAGE gels were digested using the MassPrep II Proteomics Workstation (Micromass, UK) following a procedure described previously (Sheoran 2005). Briefly, protein gel bands were cut into about 1 mm3 pieces and placed into 96-well plates. Gel bands are destained twice (for 10 min each) with 100 μL of 1:1 (v/v) ammonium bicarbonate:acetonitrile. Protein reduction was performed for 30 min at 37° C. with the addition of a solution containing 10 mM DTT and 0.1 M ammonium bicarbonate. Alkylation was achieved by the addition of 50 μL 55 mM iodoacetamide/0.1 M ammonium bicarbonate and incubation for 20 min at 37° C. Gel pieces were washed with 100 mM ammonium bicarbonate and dehydrated with acetonitrile followed by the addition of saturation with 25 μL of 6 ng/μL trypsin prepared in 50 mM ammonium bicarbonate. Digestion was carried out at 37° C. for 5 h. Peptides were extracted with 30 μL of a solution containing 0.1% trifluoroacetic acid and 3% acetonitrile for 30 min. This step was followed by two extractions with 24 μL of an aqueous solution containing 0.1% trifluoroacetic acid and 50% acetonitrile for 30 min. The combined extracts were lyophilized and reconstituted in 40 μL of a solution containing 0.2% formic acid and 3% acetonitrile prior to analysis by mass spectrometry.
Generation of an Expressed Sequence Tag Collection for S. vaccaria
A collection of S. vaccaria developing seed expressed sequence tags based on Roche 454 sequencing technology was developed as follows. Stage 1 developing seed embryos were collected and frozen at −80° C. from S. vaccaria plants grown under greenhouse conditions at the Plant Biotechnology Institute in Saskatoon, SK, Canada. The protocol of Gambino et al. (Gambino 2008) was modified for the total RNA isolation from S. vaccaria developing seeds. For the rapid CTAB-based procedure, 0.6 mL of extraction buffer containing 2% cetyltriethylammonium bromide (CTAB), 2.5% polyvinylpyrrolidone (Mr=40,000), 2 M NaCl, 100 mM Tris-HCl, pH 8.0, 25 mM EDTA and 2% of β-mercaptoethanol (added just before use) was heated at 65° C. in a microcentrifuge tube. One hundred and fifty milligrams of developing seeds were ground in liquid nitrogen and added to the extraction buffer and the tube was incubated at 65° C. for 10 min. The sample was extracted two times with chloroform isoamyl alcohol (24:1 v/v) and 0.25 volumes of 3 M LiCl was added. The mixture was kept on ice for 30 min and centrifuged at 20,000 g for 20 min at 4° C. The pellet was resuspended in 0.5 mL of SSTE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% SDS, 1 M NaCl) and extracted with 0.5 mL of chloroform/isoamyl alcohol (24:1, v/v). Cold isopropanol (0.7 volumes) was added and the sample was centrifuged at 20,000 g for 15 min at 4° C. The pellet was washed with 70% ethanol, dried and resuspended in diethylpyrocarbonate-treated water.
A collection of expressed sequence tags was generated from cDNA prepared from the isolated RNA using Roche (Indianapolis, Ind., USA) GS-FLX Titanium Technology at the McGill and Genome Quebec Innovation Centre (Montreal, Canada) according to the manufacturer's instructions. Within the MAGPIE software system (Gaasterland 1996), sequences were assembled using Mira (Chevreux 2004) and contigs were annotated based on BLASTX searches of Genbank. The EST collection provide the basis for matching mass spectrometry data from tryptic peptides from fractionated seed extracts with cDNA sequences as follows.
Liquid Chromatography/Mass Spectrometry
For LC-ESI-MS analysis, a Quadrupole Time-Of-Flight (Q-TOF) Global Ultima™ mass spectrometer (Micromass, Manchester, UK) equipped with a nano-electrospray (ESI) source and a nanoACQUITY™ UPLC solvent delivery system (Waters, Milford, Mass., USA) was used. The mobile phase was composed from a binary solvent system of A, 0.2% formic acid and 3% acetonitrile and B, 0.2% formic acid and 95% acetonitrile. Peptides were desalted with an in-line solid-phase trap column (180 μm×20 mm) packed with 5 μm resin (Symmetry™ C18, Waters) and separated on a capillary column (100 μm×100 mm, Waters) packed with BEH130 C18 resin (1.7 μm, Waters) using a column temperature of 35° C. An injection volume of 2 to 5 μL was introduced into the trap column at a flow rate of 15 μL/min for 3 min, using A:B 99:1 and flow was diverted to waste. After desalting, the flow was routed through the trap column to the analytical column with a linear gradient of 1-10% solvent B (400 mL/min, 16 min), followed by a linear gradient of 10-45% solvent B (400 mL/min, 30 min). Unless otherwise stated, Q-TOF parameter settings consisted of a capillary voltage of 3,850 V, a cone voltage of 120 V and a source temperature of 80° C.
Samples were analyzed using Data Dependant Acquisition (DDA), which consisted of the detection of multiply charged positive ions (z=2−4) from an MS survey scan. The scan range was from m/z values of 400 to 1900, with a scan time of 1 s. Up to three MS/MS scans were triggered (collision energy ranged from 20 to 80 eV, depending on charge state and precursor m/z) from each MS scan event with a peak detection window of 4 m/z units (signal intensity threshold was 16 counts/s). In MS/MS experiments, data was acquired in continuum mode with a scan time of 1.9 s and dynamic exclusion of previously detected precursors was set at 2 min. Peptide signals corresponding to trypsin and keratin were also excluded from MS/MS data collection. To obtain high mass accuracy, the reference compound leucine enkephalin (80 nM in 1:1 acetonitrile:0.1% aqueous formic acid, Environmental Resource Associates, Arvada, Colo., USA; m/z=556.2771) was continuously introduced to a second ESI source and used for the mass calibration.
Data was processed with ProteinLynx™ Global Server 2.4 (PLGS 2.4, Waters) using RAW files from LC-ESI-MS and LC-ESI-MS/MS. PKL files were generated using ProteinLynx™ Global Server 2.4 (PLGS 2.4, Waters), and subsequently submitted to Mascot™ (Matrix Science Ltd., London, UK) for peptide searches against the NCBI nr database hosted by National Research Council of Canada (NRC, Ottawa) and a local database containing the sequence information from the 454 sequencing of S. vaccaria developing seed cDNA. In the database search parameters, a maximum of 1 miscleavage was allowed for tryptic digestion. The tolerance for precursor peptide ions was ±50 ppm and for fragment ions it was ±0.4 Da. Carbamidomethylation of cysteine was selected as a fixed modification and oxidation of methionine was used as a variable modification.
LC-MS/MS data derived from analysis of a trypsinized densely stained protein band corresponding to Mr of approximately 83,000 was used to search a database of S. vaccaria expressed sequence tags (EST). The search yielded a match to a set of contiguous cDNAs sequences obtained from 454 sequencing called c272 (from the SVASD1PC EST collection). The mass spectral data corresponded to 21 peptide sequences predicted from the c272 cDNA sequence corresponding to a coverage of 24%. The gene corresponding to c272 was named Pcy1.
Isolation of a Full-Length Pcy1 cDNA from S. vaccaria
A DNA plasmid clone of the full length open reading frame of Pcy1 was obtained as follows. First-strand cDNA was synthesized from S. vaccaria developing seed total RNA with the Omniscript™ Reverse Transcription Kit (Qiagen, Mississauga, Canada). The protocol for the reverse transcriptase polymerase chain reaction (RT-PCR) was performed according to the manufacturer's instructions using 50 ng/μL of total RNA, 1× Qiagen reaction buffer, 250 μM of each of four dNTPs, 1 μM oligo dT primer, 0.5 U/μL RNase inhibitor, and 0.2 U/μL Omniscript™ reverse transcriptase (Qiagen, Mississauga, Canada) in a final volume of 20 μL. The mixture was incubated for 60 min at 37° C. As recommended by Qiagen, 2 μL of this cDNA mix was used as template for the PCR amplification of full length Pcy1.
Molecular Cloning of Pcy1 cDNA
Gene specific forward (ATG GCG ACT TCA GGA TTC TCG (SEQ ID NO: 19)) and reverse (TCA GTC TAT CCA AGG AGC TTC AAG C (SEQ ID NO: 20)) primers were designed for polymerase chain reaction (PCR) amplification of Pcy1. PCR amplification was performed with a Mycycler™ thermal cycler (Bio-Rad) using the following thermal cycling conditions: Denaturation at 95° C. for 4 min, 35 cycles of 95° C. for 20 s annealing at 54° C. for 30 s, extension at 72° C. for 2.3 min, followed by 10 min at 72° C. The reaction consisted of 0.2 μM forward primer, 0.2 μM reverse primer, 0.2 mM dNTPs, 60 mM Tris-SO4 (pH 8.9), 18 mM ammonium sulfate, 2 mM MgSO4, 0.01 units/μL Platinum™ Taq DNA Polymerase High Fidelity (Invitrogen, Life Technologies, Mississauga, Canada), 2 μL S. vaccaria cDNA in a total volume of 50 μL. The PCR products were separated by gel electrophoresis using a 0.8% Ultra™ Pure agarose gel (Invitrogen, Life Technologies, Mississauga, Canada). The PCR reaction produced a single DNA band of approximately 2.2 kb. The PCR product corresponding to this band was purified with the QIAquick™ PCR Purification Kit (Qiagen, Mississauga, Canada). Two μL of the purified PCR product was recombined with pCRB/GW/TOPO™ using a TA Cloning™ Kit (Invitrogen, Life Technologies, Mississauga, Canada) according to the manufacturer's instructions. The resulting plasmid was used to transform ONE SHOT™ TOP 10 competent E. coli cells (Invitrogen, Life Technologies, Mississauga, Canada) which were then grown overnight on Luria broth (LB) agar plates containing 100 μg/mL spectinomycin. Colony PCR, using the gene-specific open reading frame primers was used to screen for positive clones, which were then sequenced with T7 forward and reverse primers to verify the insert direction and sequence identity with respect to the c727 contig identified as putative Pcy1. Sequencing confirmed that the clone pCB006 contains a full length Pcy1 ORF (see
In pCB008, which is derived from pCB006, the Pcy1 ORF is arranged in-frame with an N-terminal His6-tag sequence. Overnight 1 mL LB cultures of E. coli BL21-AI™ cells containing 100 μg/mL ampicillin were used to inoculate 100 mL of Overnight Autoinduction Medium (Studier 2005) containing 100 μg/mL ampicillin which was incubated at 37° C. with shaking until an OD600 of 0.4 was reached. Arabinose was then added at a concentration of 0.2% and culture growth was continued at 16° C. with agitation overnight. The cultures were centrifuged in 10 mL aliquots in 15 mL polypropylene tubes at 2,000×g at 4° C. for 10 min and the resulting cell pellets were frozen at −20° C. The pellets were resuspended in chilled 500 μL of B-Per™ Bacterial Protein Extraction Reagent (Pierce Biotechnology, Rockford, Ill., USA), then transferred to two 1.5 mL Eppendorf™ tubes for cell lysis at room temperature for 20 min. Lysis was promoted with 3 sonications for 2 min. The lysed pellet was then centrifuged (12,000 g, 4° C., 8 min) and the supernatant (soluble fraction) was mixed with an equal volume of Equilibration/Wash Buffer (50 mM sodium phosphate, 300 mM NaCl, 10 mM imidazole, pH 7.4) and added to 250 μL HisPur™ Cobalt Resin (Peirce Biotechnology, Rockford, Ill., USA) for a batch style immobilized metal affinity purification of PCY1. The Eppendorf™ tubes with the supernant and agarose resin were incubated for 30 min at 4° C. on a rotator to bind the PCY1 protein. The tubes were centrifuged at 700 g and 5 washes were performed with Equilibration/Wash Buffer which was monitored for decreasing OD280. The bound PCY1 was eluted with Equilibration buffer with imidazole concentrations of 150 mM and 300 mM in a stepwise fashion. Each eluate was concentrated to 150 μL and desalted by spin dialysis (Amicon Ultra-15 devices; Millipore, Bellerica, Mass.) following the manufacturer's protocol. Concentrated fractions were assayed for enzyme activity (production of segetalin A) and separated by SDS PAGE. The resulting gels were stained with Oriole™(Bio-Rad). The recombinant PCY1 was eluted with 150 mM imidazole and appeared to be about 90% pure.
Use of Recombinant PCY1 to Produce Cyclic Peptide
For functional characterization of PCY1, the recombinant enzyme was purified using immobilized metal affinity chromatography (IMAC) from E. coli cells harbouring the plasmid pCB008, which comprises Pcy1 in a pDEST™ 17 vector (Invitrogen-Life Technologies, Carlsbad, Calif., USA). The IMAC-purified PCY1 protein was assayed with presegetalin[14,32] followed by LC/MS analysis. Similar to plant extracts, purified PCY1 showed the formation of segetalin A and linear segetalin A in the presence of presegetalin A1[14,32] (
Silene vulgaris 454 EST dataset consists of a few hundred thousand short extended sequence tags (ESTs). These were released on Feb. 7, 2011 to the “Short Read Archive” 454: public (SRP005489). A Silene vulgaris clone (SEQ ID NO: 21) corresponding to contig c150 has a predicted amino acid sequence (SEQ ID NO: 22), which is 78.5% identical to S. vaccaria PCY1. The Silene 454 dataset is also available through the BLAST portal of the PhytoMetaSyn webpage. Further, there are two other similar S. vulgaris EST datasets in the Short Read Archive (https://trace.ddbj.nig.ac.jp/DRASearch/query?organism=Silene%20vulgaris) and the University of Virginia has a BLAST portal to their Silene vulgaris dataset (http://silenegenomics.biology.virginia.edu/search.html) from which a contig sequence with 99% amino acid sequence identity to c150 can be found. To date, there has been no disclosure of the activity of the S. vulgaris c150 contig.
Dianthus superbus 454 EST dataset contains contigs c250 (SEQ ID NO: 23) and c1141 (SEQ ID NO: 25) having predicted amino acid sequences (SEQ ID NO: 24) and (SEQ ID NO: 26), respectively, which are 79% and 77.9% identical to S. vaccaria PCY1, respectively. The Dianthus 454 dataset is available through the BLAST portal of the PhytoMetaSyn webpage. There is also a Dianthus superbus 454 EST dataset from another institution in the “Short Read Archive”, 454: public (ERP000371) (https://trace.ddbj.nig.ac.jp/DRASearch/query?organism=Dianthus+superbus&study_type=¢er_name=&platform=&show=20&sort=Study). To date, there has been no disclosure of the activity of the D. superbus c250 and c1141 contigs.
To test for activity of the homologues of S. vaccaria PCY1, two cDNAs encoding were cloned from Dianthus superbus (c250 and c1141 contigs) and one from Silene vulgaris (c150 contig) essentially as described for Saponaria vaccaria PCY1 in Example 2. These were named Dianthus superbus Pcy1-c250, Dianthus superbus Pcy1-c1141 and Silene vulgaris Pcy1-c150, Briefly, gene specific forward and reverse primers were used to PCR amplify the aforementioned contigs based on homologue identification in EST collections from Dianthus leaves and Silene roots. The Dianthus superbus (c250 and c1141 contigs) and Silene vulgaris (c150 contig) PCY1 homologues were assayed with 15 μg/mL presegetalin A1[14,32] in vitro as previously described for semi-purified plant extracts to determine whether they can catalyze the production of segetalin A from presegetalin A1[14,32]. The assays were initiated by the addition of 120 ng (c250), or 138 ng (c1141) purified recombinant Dianthus superbus or 4 μg Silene vulgaris Pcy1 respectively, in a total reaction volume of 100 μL. As shown in
In order to characterize substrate specificity of PCY1 and understand the segetalin A biosynthetic mechanism, a total of 44 substrates (Table 3) were tested for the PCY1 activity and the results are briefly summarized in Table 3. The last two columns in Table 3 summarize product type detected by LC/MS after in vitro assays (CP is cyclic peptide and LP is linear peptide, +=presence, −=absence, NA=not applicable). The 44 substrates were classified as follows:
Dianthus Precursor A[14,33]
Dianthus Precursor B[14,32]
Presegetalin A1[14,32], a Wild Type (WT) Precursor of Segetalin A
No. 1 in Table 3, presegetalin A1[14,32] is the 19 amino acid WT precursor for S. vaccaria PCY1. The initial 6 amino acids correspond to the mature cyclic peptide, segetalin A. When the PCY1 was tested with its WT precursor, segetalin A and the linear form (linear peptide) of segetalin A were produced. In LC/MS, the cyclic peptide was detected as diagnostic ions m/z 610.5 (M+H)+, 632.5 (M+Na)+ and 648.5 (M+K)+, while the linear peptide was detected as m/z 628.5 (M+H)+ and 650.5 (M+Na)+ diagnostic ions. Furthermore, their presence was confirmed by MS/MS. As the cyclic peptide is the product of interest, the PCY1 activity was defined on the basis of total amount of segetalin A produced. The PCY1 activity under optimized assay condition was measured as 3 nmol/mg of protein/min.
Truncated Peptide Mutants of Presegetalin A1[14,32]
Five truncated peptide mutants were synthesized by removing various sets of amino acids from the C-terminal end of presegetalin A1[14,32] (No. 2 to 6, Table 3) to explore the importance of the C-terminal region of the substrate in the cyclization reaction. Notably, none of the truncated peptide mutants were converted into cyclic peptide by PCY1. However, No. 2, 3 and 4 showed linear peptide formation almost equivalent to the linear peptide formed from the WT substrate (No. 1). The presence of linear peptide was confirmed by MS/MS analysis. These in vitro assay results with truncated peptide mutants helped to build a hypothesis that the last two amino acids (PV) located at the C-terminal end of presegetalin A1[14,32] play an important role in the cyclization reaction.
Alanine Scanning Mutants Corresponding to Variants of the Mature Segetalin A Sequence
Mutants of the part of presegetalin A1[14,32] corresponding to mature segetalin A sequence of segetalin A (No. 7 to 12) were synthesized to determine the importance of each amino acid at particular positions. Each amino acid in segetalin A was replaced with alanine consecutively, and the alanine in the segetalin A sequence was replaced with valine. In vitro assays with these mutant peptides revealed that the PCY1 from S. vaccaria was able to make cyclic peptides from No. 7 to No. 11, however neither cyclic peptide nor linear peptide was detected when alanine was replaced with valine at the extreme C-terminal end of mature cyclic peptide (No. 12;
Dianthus superbus PCY1-c250 was also assayed with the alanine scan mutants and the activities were compared with those of S. vaccaria PCY1. D. superbus PCY1-c250 activity was comparable to that of S. vaccaria PCY1 with two notable differences. Firstly, there was no detectable cyclic peptide made from No. 7 by D. superbus PCY1-c250, although similar to S. vaccaria PCY-1 a large amount of linear peptide was detected. Secondly, D. superbus PCY1-c250 appeared to produce relatively more cyclic peptide than did S. vaccaria PCY1 from No. 11.
Alanine Scanning Mutants of the C-Terminal Region of Presegetalin A1[14,32]
In vitro assays with truncated mutants suggested the importance of the C-terminal region of presegetalin A1[14,32] in the cyclization of segetalin A. Considering this observation, 13 mutant peptides were designed (No. 13 to 25) by substitution of each amino acid with alanine in the last 13 amino acids of the presegetalin A1[14,32] sequence. When alanine was present in the sequence, it was substituted with valine. All mutant peptides were assayed with S. vaccaria PCY1 in optimized assay conditions. In the LC/MS analysis, the cyclic peptide was detected as diagnostic ions m/z 610.5 (M+H)+, 632.5 (M+Na)+ and 648.5 (M+K)+, while linear peptide was detected as m/z 628.5 (M+H)+ and 650.5 (M+Na)+ diagnostic ions. The cyclic peptide and linear peptide products were quantified with a standard curve plotted with known amounts of standards for cyclic peptide and linear peptide, respectively.
The experimental results (
Above it was observed that the removal of last two amino acids (PV) from presegetalin A1[14,32] prevented cyclic peptide formation. When these last two amino acids were substituted separately with alanine, the P31A mutant (No. 24 in Table 3) was found to yield □11 times less segetalin A than that produced from the WT substrate. On the basis of the activity of S. vaccaria PCY1 on substrates previously discussed, it would appear that the proline at position 31 in presegetalin A1[14,32] is a critical amino acid in the cyclization reaction.
At the same time, it is important to note that the substitutions at positions 25, 26 and 29 (No. 18, 19 and 22) yielded relatively higher amounts of segetalin A than that produced from WT substrate. The maximum increase in segetalin A production was observed for the S29A mutant (No. 22 in Table 3), which yielded a 30% increase in segetalin A production relative to wild type presegetalin A1[14,32].
The effect of alanine scanning showed less dramatic differences in linear peptide (linear segetalin A) production when compared to those observed with the cyclic peptide (segetalin A) production. S. vaccaria PCY1 showed a relative increase in production of linear segetalin A from all mutant substrates except with No. 13 and No. 14 when compared to that from WT (
D-Amino Acid Mutants Corresponding to Variants of the Mature Segetalin A Sequence
Gadhiri et al. (Gadhiri 1993) and Hourani et al. (Hourani 2011) have reported that cyclic peptides containing an even number of amino acids with the alternating D- and L-chirality are able to form nanotubes, some of which have antimicrobial activity and other interesting commercial properties. Given this, it was of interest to see whether D-amino acids can be tolerated in the presegetalin A1[14,32] so as to give rise to segetalin A with variant stereochemistry.
Seven mutant peptides containing D-amino acids were synthesized (No. 26 to 32 in Table 3) and tested with S. vaccaria PCY1 under optimized in vitro conditions. In initial experiments, each amino acid corresponding to segetalin A was substituted with its D-amino acid consecutively from position 15 to 19 (No. 26 to 30). Glycine at position 14 is achiral and no substitution was required. In vitro assay results revealed that the PCY1 can tolerate all L- to D-substitutions except at position 19 (No. 30) where neither cyclic peptide nor linear peptide were detected in the LC/MS analysis (
Insertion Mutants Corresponding to Variants of the Mature Segetalin A Sequence
The largest known Caryophyllaceae-like cyclic peptide (Stelladein A, cyclo-(PPPLLGPPYYG)-; SEQ ID NO: 75) is made up 11 amino acids according to Tan and Zhou (Tan 2006). This fact led us to investigate whether PCY1 can produce versions of segetalin A with extra amino acids.
A mutant peptide was synthesized with insertion of an extra alanine between position 16 and 17 (No. 33) in presegetalin A1[14,32] and assayed with PCY1. The cyclic peptide and linear peptide with 7 amino acids were both detected with LC/MS analysis of the in vitro assay. The cyclic peptide with additional alanine cyclo-(GVPAVWA) (SEQ ID NO: 76) was detected as diagnostic ions m/z 681.5 (M+H)+ and 703.5 (M+Na)+ while the linear peptide was detected as m/z 699.5 (M+H)+ and 721.5 (M+Na)+ (
As an insertion of one alanine in presegetalin A1[14,32] was tolerated, a modified presegetalin A1[14,32] peptide with three alanine insertions between position 16 and 17 was synthesized (No. 34 in Table 3) and tested with S. vaccaria PCY1 for its ability to produce the cyclized 9 amino acid product. The LC/MS analysis confirmed that PCY1 produced the expected 9 amino acid cyclic peptide (confirmed by MS/MS analysis) and linear peptide products from No. 34 This result demonstrates that S. vaccaria PCY1 can tolerate three extra amino acids.
Other A-Class and F-Class of Presegetalins
There are 9 different segetalins, divided into two groups which were designated A- and F-class segetalins. The A-class includes segetalins A, B, D, G, H, K and L while the F-class includes segetalins F and J (No. 41 and 42). The A-class cyclic peptides are comprised of 5 to 7 amino acids, of which glycine is the first amino acid in the corresponding presegetalin. In contrast, the F-class cyclic peptides are comprised of 9 amino acids, of which phenylalanine is the first amino acid in the corresponding.
Of the 8 presegetalins (No. 1, 35, 36, 38, 39, 40, 41 and 42, Table-3) assayed with S. vaccaria PCY1, cyclic peptide products were detected from all of them (
In addition, proline at the 20th position was replaced with glutamine in presegetalin D1[14,31] sequence (No. 37) and assayed with S. vaccaria PCY1 as a substrate candidate. Interestingly, the proline to glutamine substitution in No. 37 resulted in a 5 amino acid cyclic peptide product (cyclo(GLSFA); SEQ ID NO: 77), and the substituted glutamine was not part of the final cyclic peptide.
Cyclic Peptide Precursors from a Dianthus caryophyllus
Condie et al. (Condie 2011) had reported two putative cyclic peptide precursors from Dianthus caryophyllus. The amino acid sequences of these two precursors (No. 43 and 44 in Table 3) appeared to be similar to the A-class segetalin precursors. The activity of S. vaccaria PCY1 was tested on No. 43 and 44. Analysis of the assays indicated there was a small amount of cyclic peptide production from No. 43 but none from No. 44. The cyclic peptide produced from No. 43 was detected by LC/MS as diagnostic ions as m/z 732.5 (M+H)+ and m/z 754.5 (M+Na)+ and its presence was further confirmed by MS/MS analysis.
Free Listing of Sequences:
Dianthus Precursor A
Dianthus Precursor B
The Contents of the Entirety of Each of which are Incorporated by this Reference.
Other advantages that are inherent to the structure are obvious to one skilled in the art. The embodiments are described herein illustratively and are not meant to limit the scope of the invention as claimed. Variations of the foregoing embodiments will be evident to a person of ordinary skill and are intended by the inventor to be encompassed by the following claims.
This application is a national entry of International Patent Application PCT/CA2012/001130 filed Dec. 7, 2012 and claims the benefit of U.S patent application Ser. No. 61/567,844 filed Dec. 7, 2011 and U.S. patent application Ser. No. 61/640,115 filed Apr. 30, 2012, the entire contents of all of which are herein incorporated by reference.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CA2012/001130 | 12/7/2012 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2013/082708 | 6/13/2013 | WO | A |
| Number | Date | Country |
|---|---|---|
| 102174530 | Sep 2011 | CN |
| 2007103739 | Sep 2007 | WO |
| 2010130030 | Nov 2010 | WO |
| 2011005598 | Jan 2011 | WO |
| Entry |
|---|
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| Schmidt et al., Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella., Proc Natl Acad Sci U S A. (2005), vol. 102(20), pp. 7315-7320. |
| Q52QJ1-patG from Prochloron (last viewed on Mar. 11, 2015). |
| GenBank AGL51088.1 (May 18, 2013). |
| Jaillon et al., The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla., Nature (2007), vol. 449, pp. 463-467. |
| Guo et al., Protein tolerance to random amino acid change, 2004, Proc. Natl. Acad. Sci. USA 101: 9205-9210. |
| Lazar et al., Transforming Growth Factor α: Mutation of Aspartic Acid 47 and Leucine 48 Results in Different Biological Activity, 1988, Mol. Cell. Biol. 8:1247-1252. |
| Hill et al., Functional Analysis of conserved Histidines in ADP-Glucose Pyrophosphorylase from Escherichia coli, 1998, Biochem. Biophys. Res. Comm. 244:573-577. |
| Wacey et al., Disentangling the perturbational effects of amino acid substitutions in the DNA-binding domain of p53., Hum Genet, 1999, vol. 104, pp. 15-22. |
| Easton et al. (Glycosylation of Proteins-Structure, Function and Analysis., Life Science Technical Bulletin (Jul. 2011), Issue 48, pp. 1-5. |
| Number | Date | Country | |
|---|---|---|---|
| 20140363844 A1 | Dec 2014 | US |
| Number | Date | Country | |
|---|---|---|---|
| 61640115 | Apr 2012 | US | |
| 61567844 | Dec 2011 | US |
