Efficient backbone cyclization of linear peptides by a recombinant asparaginyl endopeptidase

Abstract

Cyclotides are diverse plant backbone cyclized peptides that have attracted interest as pharmaceutical scaffolds, but fundamentals of their biosynthetic origin remain elusive. Backbone cyclization is a key enzyme-mediated step of cyclotide biosynthesis and confers a measure of stability on the resultant cyclotide. Furthermore, cyclization would be desirable for engineered peptides. Here we report the identification of four asparaginyl endopeptidases (AEPs), proteases implicated in cyclization, from the cyclotide-producing plant Oldenlandia affinis. We recombinantly express OaAEP1_b and find it functions preferably as a cyclase by coupling C-terminal cleavage of propeptide substrates with backbone cyclization. Interestingly, OaAEP1_b cannot cleave at the N-terminal site of O. affinis cyclotide precursors, implicating additional proteases in cyclotide biosynthesis. Finally, we demonstrate the broad utility of this enzyme by cyclization of peptides unrelated to cyclotides. We propose that recombinant OaAEP1_b is a powerful tool for use in peptide engineering applications where increased stability of peptide products is desired.

ARTICLE

Received 4 Aug 2015 | Accepted 16 Nov 2015 | Published 18 Dec 2015

DOI: 10.1038/ncomms10199 OPEN

Efcient backbone cyclization of linear peptides by a recombinant asparaginyl endopeptidase

Karen S. Harris1,*, Thomas Durek2,*, Quentin Kaas2, Aaron G. Poth2, Edward K. Gilding2, Brendon F. Conlan1,w, Ivana Saska2, Norelle L. Daly2,w, Nicole L. van der Weerden1, David J. Craik2 & Marilyn A. Anderson1

Cyclotides are diverse plant backbone cyclized peptides that have attracted interest as pharmaceutical scaffolds, but fundamentals of their biosynthetic origin remain elusive. Backbone cyclization is a key enzyme-mediated step of cyclotide biosynthesis and confers a measure of stability on the resultant cyclotide. Furthermore, cyclization would be desirable for engineered peptides. Here we report the identication of four asparaginyl endopeptidases (AEPs), proteases implicated in cyclization, from the cyclotide-producing plant Oldenlandia afnis. We recombinantly express OaAEP1b and nd it functions preferably as a cyclase by coupling C-terminal cleavage of propeptide substrates with backbone cyclization. Interestingly, OaAEP1b cannot cleave at the N-terminal site of O. afnis cyclotide precursors, implicating additional proteases in cyclotide biosynthesis. Finally, we demonstrate the broad utility of this enzyme by cyclization of peptides unrelated to cyclotides. We propose that recombinant OaAEP1b is a powerful tool for use in peptide engineering applications where increased stability of peptide products is desired.

1 Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia. 2 Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia. * These authors contributed equally to this work. w Present addresses: Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200,

Australia (B.F.C.); Centre for Biodiscovery and Molecular Development of Therapeutics, AITHM, James Cook University, Cairns, Queensland 4878, Australia (N.L.D.). Correspondence and requests for materials should be addressed to M.A. (email: mailto:[email protected]

Web End [email protected] )

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ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms10199

Proteases are abundant throughout nature and are essential for a wide range of cellular processes. They typically serve to hydrolyse polypeptide chains, resulting in either

degradation of the target sequence or maturation to a biologically active form. Less frequently, proteases can also ligate polypeptides, producing new or alternatively spliced variants. This unusual function has been reported for processes such as the maturation of the lectin concanavalin A1, peptide presentation by major histocompatibility complex class I molecules2, and anchoring of bacterial proteins to the cell wall3. Recently, this enzymatic transpeptidation has also been implicated in the backbone cyclization of ribosomally synthesized cyclic peptides410.

Cyclotides are a well-studied class of gene-encoded cyclic peptides that are expressed in plants and exhibit a range of bioactivities including insecticidal, nematicidal and molluscicidal activity against agricultural pests1114. Structurally, they are characterized by a cyclic cystine knot motif that confers exceptional stability. Importantly, this stable framework can be used as a pharmaceutical scaffold, and bioactive sequences have been successfully grafted into cyclotides15. Backbone cyclization can also endow peptides with oral bioavailability, suggesting that this modication might nd broad application in peptide drug engineering1618. However, in vitro cyclization of synthetic peptides is challenging and the limited availability of enzymes capable of this process is a hurdle to large-scale production19,20. Furthermore, expression yields of cyclotides in transgenic plants that are not native cyclotide producers is poor, impeding transfer of agriculturally relevant bioactivities to other plants8,21. The mechanism of enzymatic cyclization intrinsic to cyclotide biosynthesis is poorly understood. Elucidating it will be important for the realization of the pharmaceutical and agricultural potential of cyclotides and for increasing the cyclization efciency of unrelated designed bioactive peptides.

Cyclotides are produced as precursors in which the cyclotide sequence is anked by N- and C-terminal propeptides (Fig. 1). It is thought that enzymatic removal of the N-terminal propeptide precedes the nal maturation step of C-terminal propeptide cleavage and ligation of the free N- and C-termini8,21. Only four native cyclases have been identied to date and the best characterized of these is the serine protease PatG, which cyclizes the bacterial cyanobactins47. In plants, the serine protease PCY1 cyclizes the segetalins; cyclic peptides from the Caryophyllaceae4. However, in the two other classes of plant-derived cyclic peptides (cyclotides and the PawS-derived cyclic peptides), strong Asx sequence conservation at the C-terminal P1 site implicates as possible cyclases the asparaginyl endopeptidases (AEPs), a group of cysteine proteases also known as vacuolar processing enzymes or Legumains, and this hypothesis is supported by studies in transgenic plants8,9,21,22.

Recently, an AEP (butelase 1) was isolated from the cyclotide-producing plant Clitoria ternatea and shown to cyclize a modied precursor of the prototypical cyclotide, kalata B1 (kB1) from Oldenlandia afnis, however, recombinant expression of functionally active butelase 1 has not been achieved, limiting its application5. Only one AEP with any cyclizing ability has been produced recombinantly, and this enzyme was highly inefcient, producing mainly hydrolysed substrate10. Here we report the identication, recombinant production and characterization of anO. afnis AEP that preferentially functions as a cyclase. The enzyme can cyclize native kalata substrate precursors and the unrelated anti-malarial peptide, R1, at close to 100% efciency. This AEP releases the C-terminal propeptide of kB1, but it does not mediate the N-terminal processing event, which must occur rst if efcient cyclization is to take place. Moreover, its specicity for model peptides mirrors the sequence requirements for cyclization of kB1 in transgenic plants, supporting a native function in the maturation of O. afnis cyclotides8,21.

ResultsIdentication and recombinant expression of O. afnis AEPs. Three expressed AEP isoforms were identied in an O. afnis complementary DNA library (OaAEP1-3) and a fourth sequence, with a single nucleotide change from OaAEP1 (resulting in a Glu371Val variant), was identied from genomic DNA (OaAEP1b) (Fig. 2a; Supplementary Fig. 1). The four isoforms share at least 77% identity at the protein level, as determined by pairwise protein alignments. When compared with butelase 1, 6469% identity was observed, whereas identity with human legumain was 4953%.

OaAEP1b was expressed in Escherichia coli as a His6-ubiquitin-AEP1b fusion protein (Supplementary Fig. 2a). AEPs are usually produced as zymogens that are self-processed at low pH to their mature, active form2325. Consistent with this processing, activity of rOaAEP1b against an internally quenched uorescent (IQF)

peptide representing the native C-terminal processing site in kB1 (Table 1; wildtype (wt)) was markedly increased following incubation at pH 4.5 (Fig. 2b). After purication, a dominant band of B32 kDa was evident by reducing SDSpolyacrylamide gel electrophoresis (PAGE) and conrmed to be rOaAEP1b by

Western blotting (Fig. 2c; Supplementary Fig. 2b). The average total protein yield from two independent experiments was B1.8 mg l 1 after activation and purication, however batch to batch variation in purity was observed. Although glycosylation of some AEPs has been reported26, the production of an active form in E. coli conrms that this is not a requirement for activity ofO. afnis AEP1b.

Mass spectrometry (MS)/MS sequencing of peptide fragments generated from tryptic, chymotryptic or endoGlu-C digestion of the activated enzyme identied several peptide fragments with non-canonical cleavage sites, suggesting that they may be derived from rOaAEP1b auto-processing events (Supplementary Fig. 2). This allowed Asp52 to be assigned as the likely N-terminal auto-processing site and Asp328, Asn329, Asp334, Asn336, Asp349 and/ or Asp351 as potential C-terminal processing sites (Fig. 2a; Supplementary Fig. 2). No peptides downstream of Asp351 were identied, indicating that the activation was essentially complete and that the C-terminal domain (Leu352Pro474) was removed during the post-activation purication step. The theoretical mass of the processed forms (30.432.8 kDa) is in good agreement with that determined by SDSPAGE/Western blotting (Fig. 2c).

Consistent with cysteine proteases of this class, rOaAEP1b was inhibited by iodoacetamide (1 mM), but was not affected by E64 (250 mM) or pepstatin A (10 mM) (Supplementary Fig. 3).

Ac-YVAD-CHO (500 mM), a caspase-1 inhibitor reported to also

ER SP NTPP Cyclotide domain (Gly1-Asn29) CTPP

CTRN GLPS P4P1P1P4

LQLK GLPV

P1P4

Figure 1 | Schematic representation of the Oak1 gene. The precursor protein encoded by the Oak1 gene is proteolytically processed to mature kB1. . indicates the N- and C-terminal processing sites. rOaAEP1b targets the C-terminal processing site. The C-terminal P1/P10 - P4/P40 sites are indicated. P100-P400 denote the N-terminal residues that replace the P10-P40 residues on release of the C-terminal propeptide. CTPP, C-terminal propeptide; ER SP, endoplasmic reticulum signal peptide; NTPP, N-terminal propeptide.

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NATURE COMMUNICATIONS | DOI: 10.1038/ncomms10199 ARTICLE

a

1-

41-

81-

121-

161-

201-

241-

281-

321-

361-

401-

441-

b c

RFU (relative to initial)

250

200

150

100

50

inhibit AEPs27, was a poor inhibitor of the recombinant enzyme suggesting that at least some P0 residues are important for active site targeting.

Substrate specicity. The activity of rOaAEP1b against IQF peptides representing wt and mutant versions of the native kB1 C-terminal cleavage site was determined (Table 1; Supplementary Fig. 4a). Along with the strict P1 Asx specicity characteristic of AEPs24, rOaAEP1b exhibited strong P20 selectivity since after

Leu31Ala substitution within the IQF peptide barely any hydrolysis was observed. This observation is consistent with the lack of cyclic product generated when the corresponding mutation was introduced in planta21. Kinetic parameters (Vmax,

Km and kcat) are reported where applicable (Table 1). The turnover rates (kcat) reported here (B0.061.6 min 1) are much slower than that reported for recombinant human legumain assayed against a small substrate (B8 s 1) (ref. 28). This is not unexpected given that rOaAEP1b prefers to carry out cyclization, rather than the hydrolysis being measured here. Supporting the observed P20 selectivity, rOaAEP1b was unable to cleave the generic AEP substrate Z-AAN-MCA (Supplementary Fig. 5).

The substrate specicity of rOaAEP1b was compared with that of recombinant human legumain (rhuLEG; Supplementary Fig. 4b)29. A stringent P1 Asx requirement was again observed; however, in contrast to rOaAEP1b, rhuLEG cleaved the Leu31Ala substrate at a rate similar to the wt substrate, demonstrating that P20 specicity is not a feature of all AEPs.

Cyclization of kB1 precursors. To explore the cyclization ability of rOaAEP1b, processing of correctly folded (as determined by

NMR) synthetic kB1 precursors was assessed by MS. When incubated with the wt kB1 precursor carrying the native C-terminal pro-hepta-peptide (GLPSLAA), the active enzyme produced a peptide of 2,891.2 Da (monoisotopic, [M H] ),

consistent with the expected mass of mature, cyclic kB1 (Fig. 3a). This product was conrmed to be identical to native kB1 by reversed phase-high performance liquid chromatography (RP-HPLC) co-elution (Supplementary Fig. 6) and one- and two-dimensional-NMR experiments (Supplementary Fig. 7). Kinetic parameters (s.e.m.) for the processing of the wt kB1 precursor were 0.53 (0.1) s-1 for kcat, 212 (76) mM for Km and 2,500 M 1 s 1 for kcat/Km as determined from a

MichaelisMenten plot (Supplementary Fig. 8). While the turnover rate (kcat) is lower than that reported for the plant-derived

KDa i ii

KDa

50 50

37 37

25 25

20 20

0 Pre-activation

Post-activation

Figure 2 | Expression of active rOaAEP1b in E. coli. (a) Sequence of OaAEP1b predicted from O. afnis genomic DNA. Predicted ER signal sequence shown in red; N-terminal propeptide shown in blue; the putative signal peptidase cleavage site is indicated by r and autocatalytic

processing sites by .. The mature OaAEP1 cyclase domain is underlined and the C-terminal auto-processing region is indicated with broken underline. The putative catalytic dyad is shown in bold and labelled with *. (b) An rOaAEP1-containing anion exchange fraction pre-and post-activation at pH 4.5 (5 h, 37 C) was tested for activity against the wt IQF peptide (14 mM). Baseline uorescence from a no substrate control has been subtracted and the relative uorescence intensity (RFU) at t 90 min is

reported. The average of two technical replicates is shown and error bars report the range (c) Activated rOaAEP1b puried by cation exchange was analysed by SDSPAGE and (i) Instant blue staining or (ii) Western blotting with anti-OaAEP1b (residues D47P474) polyclonal rabbit serum.

Table 1 | Kinetic parameters of IQF peptide cleavage by rOaVPE1b.

IQF peptide Sequence* Vmax (nmoles min-1 mg-1 protein) (s.e.m.)w Km (lM) (s.e.m.)w kcat (min-1) (s.e.m.)w,z wt Abz-STRNkGLPS-Y(3NO2) 51.3 (5.8) 55.0 (6.4) 1.6 (0.2)

R28A Abz-STANkGLPS-Y(3NO2) 6.9 (0.6) 13.0 (2.4) 0.2 (0.02) R28K Abz-STKNkGLPS-Y(3NO2) 29.3 (3.5) 42.0 (4.0) 0.9 (0.1) N29A Abz-STRAkGLPS-Y(3NO2) NAy

N29Q Abz-STRQkGLPS-Y(3NO2) NAy

N29D Abz-STRDkGLPS-Y(3NO2) B2|| ND|| B0.06|| G30A Abz-STRNkALPS-Y(3NO2) 51.0 (2.0) 29.0 (1.4) 1.6 (0.07) G30S Abz-STRNkSLPS-Y(3NO2) 35.5 (2.7) 31.4 (2.5) 1.1 (0.08)

L31A Abz-STRNkGAPS-Y(3NO2) NAy

L31I Abz-STRNkGIPS-Y(3NO2) NDz NDz NDz

IQF, internally quenched uorescent; NA, no activity; ND, not determined.

*IQF peptide residues are numbered according to their position within the native kB1 precursor, where the mature cyclotide incorporates Gly -Asn ; native Cys is substituted with Ser to avoid unpaired

Cys residues.

wNZ 3;standard error of the mean (s.e.m.)

zk is a conservative estimate assuming that the total concentration of active enzyme is equal to the total protein concentration in the enzyme preparation and an enzyme mass of 32 kDa.

yNo activity detected under the conditions tested (up to 80 mM substrate; up to 6 h incubation).

||Low V precluded accurate estimation of kinetic parameters.

zK above the range of the substrate concentrations used in this analysis precluded accurate estimation of kinetic parameters.

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a

Cyc (2,891.2)

+6 Da

Pre

m/z

2,800 2,900 3,000 3,100 3,200 3,300 3,400 3,500

b

Pre (3,792.6)

Lin 99 Da

Lin (3438.6)

Cyc (3420.6)

3,200 3,300 3,400 3,500 3,600 3,700 3,800 3,900m/z

Figure 3 | Enzymatic processing products of linear kB1 precursors. (a) MALDI MS prole of a kB1 precursor (kB1wt) containing the C-terminal propeptide in the presence of rOaAEP1b (22 h incubation). The 6 Da peak was observed only in the presence of reducing agent and corresponds to the reduced form

of cyclic kB1. (b) MALDI MS prole of a kB1 precursor (kB1C&N) containing four C-terminal propeptide residues and four N-terminal propeptide residues in the presence of rOaAEP1b (20.5 h incubation). A side product originating from chemical synthesis likely represents a Val deletion ( 99 Da). Data are

representative of at least two technical replicates. X, benzoylphenylalanine. * denotes rOaAEP1b cleavage site. Observed monoisotopic masses (Da; [M H] ) for dominant peaks are listed. Cyc, cyclic product; Lin, linear product; Pre, linear precursor.

butelase 1 (17.08 s 1; ref. 5), it is far higher than that of the recombinantly expressed cyclase PatG (1 per day; ref. 7).

To determine if rOaAEP1b could also carry out the N-terminal processing required for cyclotide maturation, a kB1 precursor was tested that contained the folded cyclotide domain anked by four residues from each of the N- and C-terminal propeptides (Fig. 3b). No N-terminal processing was observed, indicating that this processing is conducted by an enzyme other than OaAEP1b. Although the bulk of the precursor remained intact after 20.5 h, the predominant processing product was a linear peptide lacking the C-terminal propeptide, demonstrating that correct N-terminal processing must occur before cyclization. Interestingly, a mass corresponding to a cyclized version of the C-terminally processed peptide (that is, C-terminal propeptide residues released, N-terminal propeptide residues remaining) was also observed, although this was the least abundant product.

Processing of modied cyclotide precursors. To further probe cyclization requirements, we tested rOaAEP1b-mediated processing of modied kB1 and kB2 precursors over time (Fig. 4). When presented within an IQF peptide, the Leu31Ala substrate analogue was not hydrolysed by rOaAEP1b (Table 1). However, the same substitution within the kB1 precursor did not preclude cyclization by rOaAEP1b, although this version was cyclized far more slowly than the wt precursor (Fig. 4a,b). Surprisingly, the presence of disulde bonds in the cyclotide precursors is not a requirement for cyclization since a kB1 substrate analogue in which all six cysteines were substituted with serines was also efciently cyclized (Fig. 4c). The absence of a dened kB1-like structure in the kB16xS mutant was conrmed by NMR spectroscopy (Supplementary Fig. 7c). Similarly, a kB2 linear

precursor with the same Cys-Ser substitutions was also efciently cyclized, conrming that enzyme activity is not specic to individual cyclotides (Fig. 4d).

In cysteine protease-mediated peptide bond hydrolysis, nucleophilic attack of a water molecule is required to resolve the acyl-enzyme thioester intermediate. However, during peptide cyclization (or transpeptidation) the substrates N-terminal amine is postulated to function as a competing nucleophile, facilitating aminolysis of the reactive thioester intermediate30. Accordingly, a kB1 precursor with an acetyl-capped N-terminal amine was processed only to a linear peptide lacking the C-terminal propeptide (Fig. 4e). This hydrolysis occurred at a slower rate than cyclization of the wt precursor (compare with Fig. 4a). Water can therefore access the active site of rOaAEP1b, but

cyclization is favoured over hydrolysis in the presence of an appropriately positioned nucleophile.

Water is excluded during cyclization. An alternative ligation mechanism, distinct from transpeptidation, was recently proposed for huLEG31). In that mechanism, initial hydrolysis of the C-terminal propeptide is followed by a separate ligation event requiring a C-terminal Asn residue in the substrate. To distinguish between these mechanisms in the case of rOaAEP1b, reactions were carried out in the presence of 18O-labelled water and the products were analysed by high-resolution MS. An isotopic shift consistent with the incorporation of 18O was evident following enzymatic hydrolysis of the N-terminal acetylated kB1 precursor to give a linear product (Fig. 5a). However, there was no isotopic shift after processing of the wt precursor to a cyclic product, suggesting that hydrolysis is unlikely to play a role in cyclization by rOaAEP1b (Fig. 5a).

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a b c d e

kB1wt kB1L31A kB16S kB26S kB1acetyl

3,518.7

3,476.9 2,801.5

3,428.9

2,864.5 3,560.9

2,951.4

1 h

2,891.2

3,534.2

5 h

2,891.4

22 h

Cyc

Pre

Cyc

Pre

Cyc

Pre

Cyc

Pre

Lin

Pre

m/z

wt

L31A

6S

6S

acetyl

Figure 4 | Modied linear kB1 and kB2 precursors are cyclized at different rates. MALDI MS spectra of (a) kB1wt, (b) kB1L31A, (c) kB16xS, (d) kB26xS and (e) kB1acetyl cyclotide precursors at 1, 5 and 22 h post-enzyme addition. Data are representative of three technical replicates. * denotes rOaAEP1b cleavage site. Observed monoisotopic masses (Da; [M H] ) for dominant peaks are listed. Boxed inset at the 22 h time point zooms in on the region containing

the processing product. Approximate positions of the monoisotopic mass of processed products is indicated by

y

. Cyc, cyclic product; Lin, linear product;

Pre, linear precursor.

rOaAEP1b can cyclise an unrelated peptide. We also investigated cyclization of other substrates structurally unrelated to cyclotides by rOaAEP1b, focussing on the anti-malarial peptide R1 (refs 32,33). This peptide was efciently cyclized following the addition of N- and C-terminal AEP recognition sequences (Fig. 6a). Sequential trimming of the added recognition residues revealed that cyclization could be achieved following the addition of only a C-terminal AsnGly Leu motif (although some linear product was also produced from this precursor) (Figs 6ad). Lys and Gln were also accepted in place of Gly at the N terminus (Figs 6ef) with little impact on yield at the time point tested. No processing of either the native R1 peptide or a modied R1 carrying the N-terminal GlyLeu motif with only an Asn at the C terminus was observed (Supplementary Fig. 9). Subsequent digestion with endoGlu-C conrmed that, in all cases, rOaAEP1b processing produced cyclic peptide (Supplementary Fig. 10). Evidence of an additional, linear, rOaAEP1b-generated cleavage product was only observed for the R1 variant without any N-terminal anking residues (Fig. 6d; Supplementary Fig. 10c).

a b

Hydrolysed product

2,950.2 2,955.2

Cyclic product

2,895.1

2,890.1

+ H218O

H218O

m/z

m/z

Figure 5 | Enzymatic cyclization excludes water. MALDI MS prole of the enzymatic processing products of (a) kB1acetyl and (b) kB1wt linear

precursors in the presence and absence of 18O-labelled water. An isotope shift indicative of 18O incorporation only occurs during hydrolysis. Observed masses of two isotopic peaks (Da; [M H] ) are indicated. Data are

representative of three technical replicates.

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a b

Cyc (3,075.1)

Cyc (2,633.7)

+22 Da

16 Da

Pre (2,821.9)

Pre (3,360.4)

3,000 3,100 3,200 3,300 3,400

2,500 2,600 2,700 2,800 2,900

2,500 2,600 2,700 2,800 2,900

c d

Pre (2,708.8)

+22 Da

+22 Da

2,400

Cyc (2,463.5)

Lin (2,481.5)

Pre (2,651.7)

2,500 2,600 2,700 2,800

e f

Cyc (2,704.8)

Cyc (2,704.8)

+22 Da

Pre (2,893.0)

Pre (2,893.0)

2,600 2,700 2,800 2,900 3,000

2,600 2,700 2,800 2,900 3,000

m/z

Figure 6 | Flanking sequence requirements for cyclization of a model peptide by rOaAEP1. (af). MALDI MS spectra of the R1 peptide (VFAEFLPLFSKFGSRMHILK) with various anking sequences 22 h post addition of rOaAEP1b. Bold residues, anking sequences. *denotes rOaAEP1b cleavage site. Observed monoiosotopic masses (Da; [MH]) are listed. 22 Da and 16 Da peaks present in some precursor and product spectra are

likely to represent Na adducts and a synthesis-derived modication respectively. Data are representative of three technical replicates. Cyc, cyclic product; Lin, linear product; Pre, linear precursor.

DiscussionThis study reports the cloning of four AEPs from the cyclotide-producing plant O. afnis; one of which was recombinantly expressed. The recombinant enzyme required self-processing to produce the active product: a cyclase that preferentially and efciently couples C-terminal processing with C- and N-terminal ligation of linear O. afnis cyclotide precursors. Furthermore, this cyclizing ability was highly efcient when transferred to an unrelated anti-malarial peptide, demonstrating broad applicability in peptide engineering.

Consistent with other auto-inhibited proteases, rOaAEP1b required proteolytic activation to achieve maximum activity (Fig. 2b). The observed N-terminal auto-processing site (Asp52) is consistent with other experimentally validated N-terminal auto-processing sites identied in jack bean AEP34, butelase 1

(ref. 5) and human legumain28,35 (Fig. 2a, Supplementary Fig. 1). In contrast, six potential C-terminal auto-processing sites (Asp328/334/349/351, Asn329/336) were observed within a region particularly rich in Asn/Asp residues (324351). This nding is in agreement with the multiple C-terminal maturation steps recently described for rhuLEG28,35. Regardless of which of these sites is relevant in planta, the instability of active AEPs above pH 6 (refs 28,29,36) will likely preclude direct production of active enzyme in E. coli. Activated rOaAEP1b proteolytically removed the C-terminal (but not N-terminal) propeptide of a kB1 precursor and resolved the acyl-intermediate in a hydrolysis-independent manner, generating a backbone cyclized product (Figs 3 and 5). rOaAEP1b could also hydrolyse precursors lacking a free N-terminal amine to produce linear products, albeit at a slower rate. Although it is unknown if

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OaAEP1b performs both these cyclase and protease activities in vivo, the observed preference for cyclization over hydrolysis suggests that it probably functions predominantly as a cyclase.

Dual protease/ligase capabilities have been reported for PatG37, a serine protease involved in cyclic peptide production in cyanobacteria, and more recently for human legumain31. Separate mechanistic pathways for hydrolysis and ligation have been proposed for human legumain: proteolysis proceeds via hydrolysis of a cysteinyl-thioester enzyme intermediate, whereas peptide ligation occurs via activation of the free peptidyl-acarboxylate through transient formation of an enzyme-linked anhydride intermediate that is subsequently resolved via aminolysis31. The catalytically critical residue for this mechanism of ligation, Asp188, is conserved in OaAEP1b, but

several lines of evidence preclude a role for this pathway in OaAEP1b-mediated peptide cyclization. First, rOaAEP1b cannot cyclize peptides carrying a free C-terminal Asn, the minimal proposed substrate requirement in the alternative pathway (Supplementary Fig. 9). Second, our H218O experiments demonstrate the absence of 18O incorporation into the cyclized product, which strongly indicates that cyclization does not follow a hydrolysis/ligation mechanism as proposed in the alternative pathway (Fig. 5). Third, our MS/MS data for rOaAEP1b show no evidence of a reactive succinimide enzyme intermediate required for formation of the substrateenzyme anhydrides31. Hence, our mechanistic data are in agreement with the traditional concerted mechanism, in which some of the energy from the (exergonic) cleavage of the C-terminal Asn-propeptide bond is preserved in the form of a thioester intermediate and used to overcome the energetically unfavourable (endergonic) peptide bond formation (cyclization) in the second step. However, alternative mechanisms may still play a role in cyclization mediated by other AEPs or with alternative substrates.

In the context of this established mechanism, C- and N-terminal proximity was thought to be crucial for cyclization to be favoured over hydrolysis8. Here we show that pre-organization of C- and N-termini in the substrate is not required by rOaAEP1b since unconstrained cyclotide precursors lacking the characteristic disulde-bonded structure are efciently cyclized (Fig. 4). Furthermore, rOaAEP1b can cyclize an anti-malarial peptide that is structurally and functionally unrelated to cyclotides following the addition of short anking sequences (Fig. 6). These ndings are consistent with the limited structural and/or sequence requirements imposed by other native cyclases on their substrates4,5,7 Conceivably, polypeptides of diverse composition and length may be cyclized by rOaAEP1b,

provided that association of the C- and N-termini is not sterically hindered.

The application of this technology is limited to peptides that can retain activity following incorporation of the additional residues required for AEP-mediated processing. While rOaAEP1b can cyclize a model peptide with only a single non-native residue incorporated to the mature peptide, this is at the cost of cyclization efciency (Fig. 6d). Understanding the interplay between the sequence requirements for efcient cyclization and retention of bioactivity for a given target peptide will be crucial to realizing the potential of AEP-mediated cyclization. Importantly, the estimated turnover rate of rOaAEP1b (kcat, 0.53 s 1;

Supplementary Fig. 8) is multiple orders of magnitude higher than the recombinantly produced cyclase PatG (1 d 1; ref. 7), supporting its widespread application in peptide engineering.

In a previous study, a conserved tripeptide motif C terminal to both the N- and C-terminal cyclotide processing sites was identied through cyclotide sequence analysis8. This motif is GlyLeuPro in the kB1 sequence, and its importance for efcient cyclization is supported by mutagenesis studies in transgenic

plants8,21. The protease specicity of rOaAEP1b reported here against IQF peptides mirrors these requirements (Table 1). At the C-terminal processing site, the P1 Asn and P20 Leu are particularly well-conserved, and both were crucial for both in planta cyclization and in vitro cleavage of model peptides. However, over the longer incubation period of the cyclization assays, a kB1 precursor with a Leu31Ala mutation was still enzymatically processed to a cyclic product (Fig. 4). It was initially proposed that the conserved Leu residue at the P20 position of cyclotides was important for preventing water from accessing the active site during cyclization. However the observed cyclization of the kB1 Leu31Ala mutant suggests that the role of a conserved bulky hydrophobic residue at the P20 position is only to promote appropriate enzymesubstrate interaction. Congruent with this hypothesis, the absence of a P20 residue renders substrates poor targets of both rOaAEP1b (cyclization and hydrolysis; Fig. 6c; Supplementary Fig. 5) and butelase 1 (at least for hydrolysis)5. In summary, our results suggest a cyclization model in which the cleaved C-terminal propeptide retains sufcient afnity to remain bound to the active site until it is displaced by the incoming N terminus of the peptide, nally leading to cyclization by resolving the acyl intermediate8,38.

This P20 requirement is not characteristic of all AEPs9,34,39 and might be a predictor of cyclization ability within this protease family. Indeed, in extracts from C. ternatea, protein fractions that were active against the generic AEP substrate Z-AAN-MCA (which does not contain a P20 residue) did not contain the cyclizing enzyme and, conversely, the butelase 1 containing fraction did not display activity against this substrate5. Here we report the presence of four unique AEP sequences in O. afnis (Fig. 2a; Supplementary Fig. 1), and demonstrate that one (OaAEP1b) is capable of cyclizing O. afnis cyclotide precursors.

Further work will investigate whether all, or a subset of, O. afnis AEPs (at least two more of which should exist to explain all the AEP contig sequences observed) exhibit this function and whether their substrate specicity is an accurate predictor of cyclization ability.

The constraints on the sequence of the incoming N terminus may not be very stringent. At least two residues with different properties are accepted in place of Gly at the P100 position by rOaAEP1b with comparable yields of cyclic product under the conditions tested (Fig. 6e,f). Butelase 1 and Pat G also exhibit promiscuity in this region5,37. Interestingly, Gly1 is highly conserved across cyclotides from different plant species, raising the possibility that selection at this position is not driven by AEP cyclase specicity. In transgenic plants, more stringent requisites were observed and no cyclic product was made from kB1 precursors with a conservative Gly1Ala mutation8. Because AEP cannot liberate the N-terminal propeptide, we hypothesize that selection at Gly1 might be driven by the putative N-terminal processing enzyme. Further analysis will be necessary to determine if this reects differences in the enzyme homologues being assayed (that is, AEPs from the model plant Nicotiana benthamiana compared with AEPs from native cyclotide producers) or experimental conditions.

In conclusion, this study unequivocally demonstrates the involvement of an AEP in maturation of native O. afnis cyclotides, advancing our understanding of the biosynthesis of this important class of cyclic peptides. Furthermore, the promiscuous yet highly efcient nature of this recombinantly produced enzyme highlights its exciting potential value as a biological tool for cyclization of a range of bioactive peptides.

Methods

Peptide substrates and inhibitors. IQF peptides containing an N-terminal o-aminobenzoic acid (Abz) group and a C-terminal 3-nitrotyrosine (Y[3NO2])

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were synthesized by Genscript at 490% purity. Control IQF peptides representing the predicted cleavage products of the wt peptide (Abz-STRN; GLPS-Y(3NO2)

were also synthesized by Genscript at 490% purity. All IQF peptides were solubilized in 25% (v/v) acetonitrile:water. The uorogenic peptide substrate Z-AANMCA (where Z is carboxybenzyl; MCA is 7-amido-4-methylcoumarin) and the caspase inhibitor Ac-YVAD-CHO (where Ac, acetyl; CHO, aldehyde) were supplied by the Peptide Institute and solubilized in dimethyl sulfoxide. The linear cyclotide precursor peptides kB1wt, kB1C&N, kB1L31A and kB1acetyl were chemically synthesized in-house by standard Fmoc solid-phase peptide synthesis. Folding and disulde formation was carried out by incubating the reduced peptides in folding buffer (100 mM ammonium bicarbonate, 50% isopropanol, 2 mM reduced glutathione, 1 mM oxidized glutathione, pH 8.2) for 3 days40. The products were isolated by RP-HPLC at 495% purity and characterized by high-resolution MS and NMR spectroscopy. Peptides kB16xS and kB26xS as well as R1 and its

derivatives were supplied by Genscript at 485% purity, as determined by RP-HPLC and MS. Peptides were dissolved in ultrapure water before analysis.

O. afnis transcriptome. Total RNA was extracted from O. afnis root, leaf and seedling tissues using a phenol extraction method. Plant material was frozen in liquid nitrogen and ground to a ne powder, which was then resuspended in buffer(0.1 M Tris-HCl pH 8.0, 5 mM EDTA, 0.1 M NaCl, 0.5% SDS, 1% 2-mercaptoethanol), extracted twice with 1:1 phenol:chloroform and precipitated by addition of isopropanol. The pellets were dissolved in 0.5 ml water and RNA was precipitated overnight at 4 C by addition of 4 M lithium chloride. The extracted RNA of each tissue was analysed by GeneWorks using the Illumina GAIIx platform. In total, 69.3 million 75 bp paired-end reads were generated. Reads were ltered with a phred condence value of Q37 and assembled into contigs using Oases41 with k-mer ranging from 4167. The assemblies were merged using cd-hit-est42, resulting in 270,000 contigs. Statistics on the depth of sequencing were madeby aligning the reads of each tissue on the contigs using BWA43. All the sequences, including one AEP, previously identied from an EST library of O. afnis were present among the contigs44. Homologues of this AEP sequence were searched using BLAST45 in the contig library using a maximum E-value of 1e-20, resulting in the identication of 371 putative AEP transcripts. These sequences could then be clustered in 13 groups sharing at least 90% sequence identity using cd-hit42.

OaAEP1-3 cloning. Full-length AEP transcripts from the O. afnis transcriptome assembly were used to design a set of primers. A single degenerate forward primer (OaAEPdegen-F, 50-ATG GTT CGA TAT CYC GCC GG-30) was sufcient to amplify all sequences since variability within the extreme 50 region of each full-length transcript was limited to a single nucleotide position. Three reverse primers (OaAEP1-R, 50-TCA TGA ACT AAA TCC TCC ATG GAA AGA GC-30;

OaAEP2-R, 50-TTA TGC ACT GAA TCC TTT ATG GAG GG-30; OaAEP3-R 50-TTA TGC ACT GAA TCC TCC ATC G-30) were designed with the aid of Primer 3 (ref. 46). Each primer set successfully amplied an AEP sequence.

To clone expressed OaAEPs, total RNA was extracted from O. afnis leaves and shoots using TRIzol (Life Technologies) and was reverse transcribed with SuperScript III reverse transcriptase (Life Technologies) according to the manufacturers instructions11. Target sequences were amplied from the resulting complementary DNA using Phusion High Fidelity Polymerase (New England BioLabs) and the primers described above under the recommended reaction conditions. Gel extracted PCR products were dA-tailed by incubation with Invitrogen Taq Polymerase (Life Technologies) and 0.5 ml 10 mM dA in the supplied buffer. The processed products were cloned into pCR8-TOPO (Life Technologies) and transformed into E. coli. Puried DNA from clones that were PCR positive for an AEP insert were sent for Sanger sequencing at the Australian Genome Research Facility (http://www.agrf.org

Web End =www.agrf.org). Coding sequences have been deposited in Genbank (accession codes: OaAEP1 (KR259377), OaAEP2 (KR259378), OaAEP3 (KR259379)).

In an alternative approach, genomic DNA was extracted from O. afnis leaf tissue using a DNeasy Plant Mini Kit according to the manufacturers instructions. PCR amplication from this DNA used primers specically targeting the OaAEP1 nucleotide sequence. Gel extracted product was dA-tailed as above, cloned into the TOPO vector and transformed into E. coli. Sequencing of PCR-positive clones identied a fourth sequence with a single amino acid change from OaAEP1 (OaAEP1b).

Antibodies. Polyclonal anti-OaAEP1b rabbit serum was generated by immunizing a New Zealand White rabbit with a denatured, inactive form of OaAEP1b (residues D47P474) that was produced recombinantly in E. coli. The rabbit received three doses, four weeks apart, of 150 mg of antigen in 50% (v/v) PBS and Freunds incomplete adjuvant. Serum was obtained 2 weeks after the nal dose and used at a 1:2,000 dilution for Western blotting.

Recombinant expression of O. afnis AEP1b (rOaAEP1b). Initial trials to produce active O. afnis AEP1b based on predicted N- and C-terminal processing sites (residues D47D420) were unsuccessful and subsequent expression attempts incorporated both N- and C-terminal prodomains. DNA encoding full-length

O. afnis AEP1b without the putative signalling domain (residues A24-P474) was inserted into the pHUE vector47 to give a His6-ubiquitin-OaAEP1b fusion protein construct (Supplementary Fig. 2) and introduced into T7 shufe E. coli cells (New England BioLabs). Transformed cells were grown at 30 C in superbroth(3.5% tryptone (w/v), 2% yeast extract (w/v), 1% glucose (w/v), 90 mM NaCl, 5 mM NaOH) to mid-log phase; the temperature was then reduced to 16 C and expression was induced with isopropyl D-1-thiogalactopyranoside (0.4 mM) for B20 h. Cells were harvested by centrifugation and resuspended in non-denaturing lysis buffer (50 mM Tris-HCl, 150 mM NaCl, 0.1% triton X 100, 1 mM EDTA, pH 7). Lysis was promoted by a total of ve freeze/thaw cycles and the addition of lysozyme (hen egg white; 0.4 mg ml 1). DNase (bovine pancreas;

40 mg ml 1) and MgCl2 (0.4 M) were also added. Cellular debris was removed by centrifugation and the lysate was stored at 80 C until required.

Purication and activation of rOaAEP1b. Lysate containing expressed rOaAEP1b was ltered through a 0.1 mm glass bre lter before being diluted 1:8 in buffer A (20 mM bis-Tris, 0.2 M NaCl, pH 7) and loaded onto two 5 ml HiTrap Q Sepharose high performance columns connected in series (GE Healthcare; 1.63.1 ml undiluted lysate per millilitre resin). Bound proteins were eluted with a continuous salt gradient (030% buffer B (20 mM bis-Tris, 2 M NaCl, pH 7); 15 column volumes) and AEP-positive fractions identied by Western blotting (anti-OaAEP1b rabbit serum (1:2,000); peroxidase-conjugated anti-rabbit IgG (GE Healthcare NA934; 1:5000)). To self-activate rOaAEP1b, EDTA (1 mM) and Tris(2-carboxyethyl)phosphine hydrochloride (0.5 mM) were added, the pH was adjusted to 4.5 with glacial acetic acid and the protein pool was incubated for 5 h at 37 C. Protein precipitation at this pH allowed removal of the bulk of the contaminating proteins by centrifugation. The remaining protein was ltered (0.22 mm), diluted 1:8 in buffer A2 (50 mM acetate, pH 4) then captured on a 1 ml HiTrap SP Sepharose high performance column (GE Healthcare). Bound proteins were eluted with a salt gradient (0100% buffer B2 (50 mM acetate, 1 M NaCl, pH 4); 10 column volumes) and AEP-positive fractions were pooled. The nal product was analysed by MS and reducing SDSPAGE followed by Western blotting and staining with Instant blue (Expedeon). The total concentration of protein was estimated by bicinchoninic acid assay according to the manufacturers instructions.

Identication of the auto-processing sites of rOaAEP1b. Aliquots of rOaAEP1b (5 ml) were diluted 1:1 with either 100 mM ammonium bicarbonate pH 8.0 (trypsin, chymotrypsin) or 100 mM ammonium phosphate pH 8.0 (endoGlu-C) and enzymatically digested with endoGlu-C, trypsin or chymotrypsin (100 ng ml 1).

Cleavages were conducted over 16 h at 37 C (endoGlu-C, trypsin) or 30 C (chymotrypsin). Injections of each digest (5 ml) were introduced to a Shimadzu nanoLC delivering a linear acetonitrile gradient at a ow rate of 500 nl min 1 for reversed-phase separation on a C18 Zorbax column (Agilent 300SB-C18, 3.5 mm particle size, 150 mm 100 mm). Column eluate was interfaced directly with a

5600 TripleTOF LC-MS/MS instrument (AB SCIEX, Canada) equipped with a nanoelectrospray ionization source.

Tandem MS data were generated in Information Dependent Acquisition experiments, wherein full-scan TOF-MS spectra were acquired for 250 ms over m/z 3501,800, and the 20 most intense signals with charge state 2 to 5 were

selected for product ion scans of duration 50 ms over m/z 801,400. Data were acquired and processed using the Analyst TF 1.6 software (AB SCIEX, Canada). Automated protein identication was performed in ProteinPilot 4.0 using the Paragon algorithm with no enzyme settings to interrogate an E. coli K12 proteome database (Uniprot) concatenated with sequences of rOaAEP1b and those of the three cleavage enzymes, with false discovery rate set at Po0.05. Spectral data for peptides software matched to rOaAEP1b were conrmed via manual interpretation in Analyst TF 1.6.

Assaying protease activity against uorescent peptides. To assay activity of rOaAEP1b against both internally quenched and other uorescent peptides, substrate and enzyme were diluted as appropriate in activity buffer (50 mM sodium acetate, 50 mM NaCl, 1 mM EDTA, 0.5 mM Tris(2-carboxyethyl)phosphine hydrochloride, pH 5). To assay activity of rhuLEG (R&D systems) against the same substrates, the enzyme was rst activated by incubation in 50 mM sodium acetate, 100 mM NaCl, pH 4 (4 ml buffer/1 ml enzyme) for 2 h at 37 C. Substrates and activated rhuLEG were diluted in 50 mM MES, 250 mM NaCl, pH 5 as required. Diluted enzyme and substrate were added to black, at bottomed microtiter plates in a total assay volume of 110200 ml. The change in uorescence intensity over time was monitored on a SpectraMax M2 (Molecular Devices) using excitation/ emission wavelengths of 320/420 nm (IQF peptides) or 360/460 nm (other uorescent peptides). Substrate and enzyme concentrations in each assay and the time point presented are as indicated in the gure legends.

To determine the kinetics of rOaAEP1b activity against IQF peptides, each substrate was assayed at a range of concentrations between 2.5 and 80 mM in a total volume of 200 ml. The total protein concentration of the enzyme preparation used in the kinetic assays was 3.5 mg ml 1. It was not possible to precisely determine the concentration of active enzyme due to impurities remaining in the preparation and the absence of an inhibitor appropriate for active site titration. However, a conservative turnover rate (kcat) was estimated based on a mass of 32 kDa and

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the assumption that the total protein concentration reected active enzyme.

At each substrate concentration, initial velocities were calculated from the linear portion of the progress curve. Km and Vmax were estimated using the Michaelis

Menten equation and the curve-tting program GraphPad Prism (GraphPad Software, San Diego).

The high peptide concentrations required for estimating kinetic parameters necessitated the use of a correction factor to account for the inner lter effect; a phenomenon where high relative concentrations of the quenching group impede detection of the signal from the uorescent donor even after substrate hydrolysis48. This was achieved as described previously48. The output generated by the uorescent hydrolysis product (Abz-STRN) was measured in the presence of each concentration of non-hydrolysed substrate. The correction factor was the ratio between the expected and observed uorescence signal at each substrate concentration. The corrected signal for each data point was then converted to amount of product by comparison to a standard curve of the uorescent hydrolysis product.

Inhibition assays. To investigate the impact of inhibitors on enzyme activity against the wt IQF peptide, rOaAEP1b (4.4 mg ml1 total protein) was incubated with the indicated concentration of E64, Ac-YVAD-CHO, pepstatin A and iodoacetamide for 40 min before addition to the substrate (11 mM). Enzyme activity against the wt IQF peptide was then assessed as described above.

Cyclization assay. Linear target peptides (280 mM) were incubated with rOaAEP1b (12 mg ml 1 total protein unless otherwise indicated) in activity buffer.

The reaction was allowed to proceed for up to 22 h at room temperature and was analysed by matrix-assisted laser desorption/ionization MS (MALDI MS), RP-HPLC or NMR as appropriate.

To conrm the presence of cyclic product, R1 derivatives processed by rOaAEP1b were subsequently digested with endoGlu-C (25 mg ml 1) in reaction buffer (50 mM Tris-HCl, 0.5 mM GluGlu, pH 8) such that the nal dilution of the cyclization mix was 1:4. The reaction was allowed to proceed for 18 h at 37 C before analysis by MALDI MS.

In heavy water experiments, isotopically labelled water (97 atom % 18O) was used in place of unlabelled water. Linear target peptides (70 mM) were incubated with rOaAEP1b (6 mg ml 1 total protein) in a non-reducing activity buffer (50 mM sodium acetate, 50 mM NaCl, 1 mM EDTA, pH 5) for 22 h at room temperature.

The nal H218O concentration in the assay was 81%.

MS to track cyclization of linear peptides. Cyclization of linear target peptides was monitored by MALDI MS. The reaction mixture (1020 ml) was desalted using C18 zip tips and eluted in 4 ml 50% acetonitrile, 0.1% triuoroacetic acid (TFA). A saturated MALDI matrix solution (acyano-4-hyroxycinnamic acid) prepared in 95% acetonitrile, 0.1% TFA was diluted 1:22 such that the nal matrix solution comprised 90% acetonitrile, 0.1% TFA and 1 mM NH4H2PO4. Eluted samples were mixed 1:4 with the MALDI matrix, spotted onto a MALDI plate and analysed by an Ultraex III TOF/TOF (Bruker) in positive reector mode.

Purication of kB1 following in vitro cyclization. The crude cyclization mixture was loaded to an Agilent Zorbax C18 reversed-phase column (4.6 250 mm,

300 ) and separated on a Shimadzu Prominence system using a linear gradient of 555% buffer B (90% acetonitrile, 10% H2O, 0.05% TFA) in buffer A (0.05%

TFA/H2O) over 60 min. Fractions were collected manually, analysed by MALDI MS essentially as described above and lyophilized. Analytical HPLC and co-elution studies with chemically synthesized kB1 were carried out as described above.

Nuclear magnetic resonance spectroscopy. All peptides were dissolved in 90% H2O/10% D2O at a concentration of B2.0 mg ml 1 (0.50.75 mM). kB1 obtained from in vitro cyclizations was dissolved at 0.3 mg ml 1 (B0.1 mM). Spectra were recorded on a Bruker Avance 600 MHz spectrometer equipped with a cryoprobe at 298 K. Phase-sensitive mode using time-proportional phase incrementation for quadrature detection in the t1 dimension was used for all two-dimensional spectra.

Excitation sculpting with gradients was used to achieve water suppression. NMR experiments included TOCSY using a MLEV-17 spin lock sequence with an 80 ms mixing time, and NOESY with a 200 ms mixing time. Spectra were recorded with 4,096 data points in the F2 dimension and 512 increments in the F1 dimension. The t1 dimension was zero-lled to 1,024 real data points, and the F1 and F2 dimensions were multiplied by a sine-squared function before Fourier transformation. The spectra were referenced to the water signal at 4.77 p.p.m. at 298 K. All spectra were processed using TopSpin (Bruker) and manually assigned with CCPNMR using the sequential assignment protocol.

Cyclization kinetics. To determine the kinetics of rOaAEP1b activity against the wt kB1 precursor, the substrate was assayed at room temperature at a range of concentrations between 75 and 250 mM in a total volume of 20160 ml of activity buffer. The total protein concentration of the enzyme preparation added to the kinetic assays was 19.7 mg ml 1. The reaction was quenched after 5 min with 0.1%

TFA and the volume adjusted to 800 ml. A volume of 700 ml was loaded onto a

reversed-phase C18 analytical column (Agilent Eclipse C18, 5 mm, 4.6 150 mm)

and peptides were separated by HPLC (19 min linear gradient of 1260% acetonitrile, 0.1% TFA at 1 ml min 1). The identity of eluted peaks was conrmed using MALDI MS. The area under the curve corresponding to the precursor peptide was quantitated by comparison to a standard curve and initial velocities were calculated by converting this to mmoles product formed. Kinetic parameters were estimated using the MichaelisMenten equation and the curve-tting program GraphPad Prism (GraphPad Software, San Diego). As for the IQF peptides, it was not possible to precisely determine the concentration of active enzyme due to impurities remaining in the preparation and the absence of an inhibitor appropriate for active site titration. However, a conservative turnover rate (kcat) was

estimated based on a mass of 32 kDa and the assumption that the total protein concentration reected active enzyme. Differences in enzyme preparations means these parameters are not directly comparable to those determined for the IQF peptides.

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Acknowledgements

We thank Ms Rosemary Guarino for assistance with expressions, Dr Pedro Quimbar and Dr Thomas Shafee for helpful discussions, Mr Owen McCorkelle and Dr Suresh Mathivanan for preliminary MS analysis, Mr James Brown for isolation of the AEP sequence from genomic DNA, Professor Michael Foley for providing the native R1 peptide, Mr Alun Jones and the Institute for Molecular Bioscience Mass Spectrometry Facility for expertise and access to MS equipment and Dr Joshua Mylne for assistance with transcriptomics. This work was supported by The Australian Research Council grants DP0984390 and DP150100443 and Hexima Ltd.

Author contributions

K.S.H. produced the recombinant enzyme and carried out cyclization assays and kinetic analysis. T.D. and N.L.D. synthesized cyclotide precursors. T.D. carried out NMR and HPLC co-elution studies. T.D., Q.K., E.K.G. and I.S. contributed to the isolation of AEP sequences. T.D. and A.G.P. carried out mass spectrometry analysis of the recombinant AEP. B.F.C. produced rabbit antiserum. K.S.H., T.D., N.L.v.d.W., D.J.C. and M.A.A. contributed to study design and data analysis. All authors contributed to the writing and/or review of the manuscript.

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How to cite this article: Harris, K. S. et al. Efcient backbone cyclization of linear peptides by a recombinant asparaginyl endopeptidase. Nat. Commun. 6:10199 doi:10.1038/ncomms10199 (2015).

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