ORCID Profile
0000-0003-1720-1282
Current Organisation
University of Queensland
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In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Proteins and Peptides | Plant Cell and Molecular Biology | Medicinal and Biomolecular Chemistry | Structural Biology (incl. Macromolecular Modelling) | Enzymes | Biochemistry and Cell Biology | Biologically Active Molecules
Expanding Knowledge in the Biological Sciences | Expanding Knowledge in the Chemical Sciences | Crop Protection Chemicals | Human Diagnostics |
Publisher: Springer Science and Business Media LLC
Date: 27-03-2020
DOI: 10.1038/S41467-020-15418-2
Abstract: Asparaginyl endopeptidases (AEPs) catalyze the key backbone cyclization step during the biosynthesis of plant-derived cyclic peptides. Here, we report the identification of two AEPs from Momordica cochinchinensis and biochemically characterize MCoAEP2 that catalyzes the maturation of trypsin inhibitor cyclotides. Recombinantly produced MCoAEP2 catalyzes the backbone cyclization of a linear cyclotide precursor (MCoTI-II-NAL) with a k cat /K m of 620 mM −1 s −1 , making it one of the fastest cyclases reported to date. We show that MCoAEP2 can mediate both the N-terminal excision and C-terminal cyclization of cyclotide precursors in vitro. The rate of cyclization/hydrolysis is primarily influenced by varying pH, which could potentially control the succession of AEP-mediated processing events in vivo. Furthermore, MCoAEP2 efficiently catalyzes the backbone cyclization of an engineered MCoTI-II analog with anti-angiogenic activity. MCoAEP2 provides enhanced synthetic access to structures previously inaccessible by direct chemistry approaches and enables the wider application of trypsin inhibitor cyclotides in biotechnology applications.
Publisher: American Chemical Society (ACS)
Date: 24-09-2014
DOI: 10.1021/JF5022847
Abstract: Grain protein composition determines quality traits, such as value for food, feedstock, and biomaterials uses. The major storage proteins in sorghum are the prolamins, known as kafirins. Located primarily on the periphery of the protein bodies surrounding starch, cysteine-rich β- and γ-kafirins may limit enzymatic access to internally positioned α-kafirins and starch. An integrated approach was used to characterize sorghum with allelic variation at the kafirin loci to determine the effects of this genetic ersity on protein expression. Reversed-phase high performance liquid chromatography and lab-on-a-chip analysis showed reductions in alcohol-soluble protein in β-kafirin null lines. Gel-based separation and liquid chromatography-tandem mass spectrometry identified a range of redox active proteins affecting storage protein biochemistry. Thioredoxin, involved in the processing of proteins at germination, has reported impacts on grain digestibility and was differentially expressed across genotypes. Thus, redox states of endosperm proteins, of which kafirins are a subset, could affect quality traits in addition to the expression of proteins.
Publisher: American Chemical Society (ACS)
Date: 18-03-2015
DOI: 10.1021/NP500802P
Abstract: Orbitides are short (5-11 amino acid residue), ribosomally synthesized homodetic plant cyclic peptides characterized by N-to-C amide bonds rather than disulfide bonds. Orbitides can be discovered using mass spectrometry of plant extracts or by identifying DNA sequences coding for the precursor protein. The number of orbitides that have been characterized to date, by a number of different research groups, is modest. The nomenclatural system currently used for the Type VI cyclic peptides has been developed in an ad hoc fashion and is somewhat arbitrary. We propose a systematic naming system specifically for the Type VI cyclic peptides that reflects the taxonomic name of the species producing the orbitides and a numbering system that enables systematic representation of amino acid residues and modifications. The proposed naming system emulates the IUPAC Nomenclature for Natural Products and UniProt, both of which use abbreviations of taxonomic names for the compounds in question. Nomenclature for post-translational modifications also follows the IUPAC precedent, as well as the cyclic peptide literature. Furthermore, the proposed system aims to maintain agreement with the precedents set by the pre-existing literature. An ex le of the proposed nomenclature is provided using the methionine-containing homodetic peptides of Linum usitatissimum (flaxseed).
Publisher: CRC Press
Date: 08-07-2014
DOI: 10.1201/B17153
Publisher: Springer Science and Business Media LLC
Date: 08-2014
Publisher: Wiley
Date: 05-2014
Publisher: Proceedings of the National Academy of Sciences
Date: 03-04-2019
Abstract: Ribosomally synthesized and post-translationally modified peptides are natural products that hold great promise for a range of medical and biotechnological applications. However, the cost-effective heterologous production of these peptides is h ered by a poor understanding of their biosynthesis. Cyclotides, plant-derived, disulfide-knotted, head-to-tail cyclic peptides, exhibit exceptional stability and great amenability for amino acid substitutions and insertions. Although much effort has been invested toward understanding cyclotide biosynthesis, details of the key proteolytic step before cyclization remained elusive for two decades. We used an activity-guided approach to discover the enzymes involved. Our characterization of these enzymes will enable efficient approaches for heterologous cyclotide production.
Publisher: Oxford University Press (OUP)
Date: 22-12-2018
DOI: 10.1093/JXB/ERX422
Publisher: Springer Science and Business Media LLC
Date: 19-09-2017
Publisher: Springer Science and Business Media LLC
Date: 05-04-2008
DOI: 10.1007/S00299-008-0543-8
Abstract: The number of viable shoots influences the overall architecture and productivity of wheat (Triticum aestivum L.). The development of lateral branches, or tillers, largely determines the resultant canopy. Tillers develop from the outgrowth of axillary buds, which form in leaf axils at the crown of the plant. Tiller number can be reduced if axillary buds are not formed or if the outgrowth of these buds is restricted. The teosinte branched1 (tb1) gene in maize, and homologs in rice and Arabidopsis, genetically regulate vegetative branching. In maize, increased expression of the tb1 gene restricts the outgrowth of axillary buds into lateral branches. In this study, the maize tb1 gene was introduced through transformation into the wheat cultivar "Bobwhite" to determine the effect of tb1 overexpression on wheat shoot architecture. Examination of multiple generations of plants reveals that tb1 overexpression in wheat results in reduced tiller and spike number. In addition, the number of spikelets on the spike and leaf number were significantly greater in tb1-expressing plants, and the height of these plants was also reduced. These data reveal that the function of the tb1 gene and genetic regulation of lateral branching via the tb1 mode of action is conserved between wheat, rice, maize and Arabidopsis. Thus, the tb1 gene can be used to alter plant architecture in agriculturally important crops like wheat.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 18-09-2020
Abstract: The pain-inducing components of Australian stinging tree venom are miniproteins that modulate voltage-gated sodium channels.
Publisher: Springer Science and Business Media LLC
Date: 17-03-2023
DOI: 10.1007/S11248-023-00341-1
Abstract: Multiple sclerosis (MS) is a debilitating disease that requires prolonged treatment with often severe side effects. One experimental MS therapeutic currently under development is a single amino acid mutant of a plant peptide termed kalata B1, of the cyclotide family. Like all cyclotides, the therapeutic candidate [T20K]kB1 is highly stable as it contains a cyclic backbone that is cross-linked by three disulfide bonds in a knot-like structure. This stability is much sought after for peptide drugs, which despite exquisite selectivity for their targets, are prone to rapid degradation in human serum. In preliminary investigations, it was found that [T20K]kB1 retains oral activity in experimental autoimmune encephalomyelitis, a model of MS in mice, thus opening up opportunities for oral dosing of the peptide. Although [T20K]kB1 can be synthetically produced, a recombinant production system provides advantages, specifically for reduced scale-up costs and reductions in chemical waste. In this study, we demonstrate the capacity of the Australian native Nicotiana benthamiana plant to produce a structurally identical [T20K]kB1 to that of the synthetic peptide. By optimizing the co-expressed cyclizing enzyme, precursor peptide arrangements, and transgene regulatory regions, we demonstrate a [T20K]kB1 yield in crude peptide extracts of ~ 0.3 mg/g dry mass) in whole plants and close to 1.0 mg/g dry mass in isolated infiltrated leaves. With large-scale plant production facilities coming on-line across the world, the sustainable and cost-effective production of cyclotide-based therapeutics is now within reach.
Publisher: AIP Publishing
Date: 08-2019
DOI: 10.1063/1.5098794
Abstract: Single-photon emitters in gallium nitride (GaN) are gaining interest as attractive quantum systems due to the well-established techniques for growth and nanofabrication of the host material, as well as its remarkable chemical stability and optoelectronic properties. We investigate the nature of such single-photon emitters in GaN with a systematic analysis of various s les produced under different growth conditions. We explore the effect that intrinsic structural defects (dislocations and stacking faults), doping, and crystal orientation in GaN have on the formation of quantum emitters. We investigate the relationship between the position of the emitters—determined via spectroscopy and photoluminescence measurements—and the location of threading dislocations—characterized both via atomic force microscopy and cathodoluminescence. We find that quantum emitters do not correlate with stacking faults or dislocations instead, they are more likely to originate from point defects or impurities whose density is modulated by the local extended defect density.
Publisher: Springer Science and Business Media LLC
Date: 03-02-2020
Publisher: Cold Spring Harbor Laboratory
Date: 24-05-2019
DOI: 10.1101/644732
Abstract: Regeneration of a limb or tissue can be achieved through multiple different pathways and mechanisms. The sea anemone Exaiptasia pallida has been observed to have excellent regenerative proficiency but this has not yet been described transcriptionally. In this study we examined the genetic expression changes during a regenerative timecourse and report key genes involved in regeneration and wound healing. We found that the major response was an early upregulation of genes involved in cellular movement and cell communication, which likely contribute to a high level of tissue plasticity resulting in the rapid regeneration response observed in this species. We find the immune system is only transcriptionally active in the first eight hours post- utation and conclude, in accordance with previous literature, that the immune system and regeneration have an inverse relationship. Fifty-nine genes (3.8% of total) differentially expressed during regeneration were identified as having no orthologues in other species, indicating that regeneration in E. pallida may rely on the activation of species-specific novel genes. Additionally, taxonomically-restricted novel genes, including species-specific novels, and highly conserved genes were identified throughout the regenerative timecourse, showing that both may work in concert to achieve complete regeneration. We conclude that E. pallida behaves similarly to other anemone species such as Nematostella vectensis and Calliactis polypus but with some notable novel differences.
Publisher: Wiley
Date: 30-08-2007
Publisher: Elsevier BV
Date: 2015
Publisher: Elsevier BV
Date: 2019
Publisher: Wiley
Date: 26-07-2012
DOI: 10.1111/J.1365-2486.2012.02767.X
Abstract: Increased seawater p CO 2 , and in turn ‘ocean acidification’ (OA), is predicted to profoundly impact marine ecosystem ersity and function this century. Much research has already focussed on calcifying reef‐forming corals (Class: Anthozoa) that appear particularly susceptible to OA via reduced net calcification. However, here we show that OA‐like conditions can simultaneously enhance the ecological success of non‐calcifying anthozoans, which not only play key ecological and biogeochemical roles in present day benthic ecosystems but also represent a model organism should calcifying anthozoans exist as less calcified (soft‐bodied) forms in future oceans. Increased growth (abundance and size) of the sea anemone ( Anemonia viridis ) population was observed along a natural CO 2 gradient at Vulcano, Italy. Both gross photosynthesis ( P G ) and respiration (R) increased with p CO 2 indicating that the increased growth was, at least in part, fuelled by bottom up (CO 2 stimulation) of metabolism. The increase of P G outweighed that of R and the genetic identity of the symbiotic microalgae ( Symbiodinium spp.) remained unchanged (type A19) suggesting proximity to the vent site relieved CO 2 limitation of the anemones' symbiotic microalgal population. Our observations of enhanced productivity with p CO 2 , which are consistent with previous reports for some calcifying corals, convey an increase in fitness that may enable non‐calcifying anthozoans to thrive in future environments, i.e. higher seawater p CO 2 . Understanding how CO 2 ‐enhanced productivity of non‐ (and less‐) calcifying anthozoans applies more widely to tropical ecosystems is a priority where such organisms can dominate benthic ecosystems, in particular following localized anthropogenic stress.
Publisher: Oxford University Press (OUP)
Date: 20-06-2022
DOI: 10.1093/JXB/ERAC273
Abstract: Plant molecular farming aims to provide a green, flexible, and rapid alternative to conventional recombinant expression systems, capable of producing complex biologics such as enzymes, vaccines, and antibodies. Historically, the recombinant expression of therapeutic peptides in plants has proven difficult, largely due to their small size and instability. However, some plant species harbour the capacity for peptide backbone cyclization, a feature inherent in stable therapeutic peptides. One obstacle to realizing the potential of plant-based therapeutic peptide production is the proteolysis of the precursor before it is matured into its final stabilized form. Here we demonstrate the rational domestication of Nicotiana benthamiana within two generations to endow this plant molecular farming host with an expanded repertoire of peptide sequence space. The in planta production of molecules including an insecticidal peptide, a prostate cancer therapeutic lead, and an orally active analgesic is demonstrated.
Publisher: Springer Science and Business Media LLC
Date: 15-01-2013
Publisher: Elsevier BV
Date: 12-2020
Publisher: Springer Science and Business Media LLC
Date: 05-11-2020
DOI: 10.1007/S00425-020-03505-Z
Abstract: We demonstrate the production of a structurally correct cyclotide in rice suspension cells with co-expression of a ligase-type AEP, which unlocks monocotyledons as production platforms to produce cyclotides. Cyclotides are a class of backbone-cyclic plant peptides that harbor a cystine knot composed of three disulfide bonds. These structural features make cyclotides particularly stable, and thus they have attracted significant attention for their use in biotechnological applications such as drug design. Currently, chemical synthesis is the predominant strategy to produce cyclotides for research purposes. However, synthetic production becomes costly both economically and environmentally at large scale. Plants offer an attractive alternative to chemical synthesis because of their lower cost and environmental footprint. In this study, rice suspension cells were engineered to produce the prototypical cyclotide, kalata B1 (kB1), a cyclotide with insecticidal properties from the African plant Oldenlandia affinis. Engineered rice cells produced structurally validated kB1 at yields of 64.21 µg/g (DW), which was dependent on the co-expression of a peptide ligase-competent asparaginyl endopeptidase OaAEP1
Publisher: Wiley
Date: 22-10-2008
Publisher: Frontiers Media SA
Date: 28-05-2019
Publisher: Frontiers Media SA
Date: 15-05-2019
Publisher: American Chemical Society (ACS)
Date: 23-12-2020
Publisher: Elsevier BV
Date: 05-2015
Publisher: Springer Science and Business Media LLC
Date: 20-06-2018
DOI: 10.1038/S41467-018-04669-9
Abstract: Asparaginyl endopeptidases (AEPs) are proteases that have crucial roles in plant defense and seed storage protein maturation. Select plant AEPs, however, do not function as proteases but as transpeptidases (ligases) catalyzing the intra-molecular ligation of peptide termini, which leads to peptide cyclization. These ligase-type AEPs have potential biotechnological applications ranging from in vitro peptide engineering to plant molecular farming, but the structural features enabling these enzymes to catalyze peptide ligation/cyclization rather than proteolysis are currently unknown. Here, we compare the sequences, structures, and functions of erse plant AEPs by combining molecular modeling, sequence space analysis, and functional testing in planta. We find that changes within the substrate-binding pocket and an adjacent loop, here named the “marker of ligase activity”, together play a key role for AEP ligase efficiency. Identification of these structural determinants may facilitate the discovery of more ligase-type AEPs and the engineering of AEPs with tailored catalytic properties.
Publisher: Elsevier BV
Date: 12-2020
Publisher: Elsevier BV
Date: 07-2009
DOI: 10.1093/MP/SSP037
Publisher: American Chemical Society (ACS)
Date: 11-02-2021
Publisher: Elsevier BV
Date: 08-2020
Publisher: Elsevier BV
Date: 03-2022
DOI: 10.1016/J.PHYTOCHEM.2021.113053
Abstract: Cyclotides are a class of ribosomally-synthesized plant peptides that function in plants as a defense against insects and fungal pathogens. Their unique structure comprises a cyclized peptide backbone threaded by three disulfide bonds, that imparts structural stability, a desirable quality for peptide-based therapeutics or insecticides. Producing these peptides synthetically is challenging due to the amount of chemical waste produced and inefficiency of folding certain cyclotides. Thus, it is desirable to develop a means to access cyclotide biosynthesis in their native hosts, cultured in defined conditions, at both laboratory and commercial scale. Here we developed suspension cell cultures from two species previously unexplored for cyclotide production in suspension cells, Clitoria ternatea L., Hybanthus enneaspermus F. Muell., as well as with Oldenlandia affinis (Roem. & Schult.) DC., a species reported previously to accumulate cyclotides in cell suspensions. We assessed the growth rate, cyclotide production and gene expression for the various species. We found that while many cyclotides had reduced expression in Oldenlandia affinis suspension cells when compared to plant organs, those in Clitoria ternatea and Hybanthus enneaspermus maintained or increased expression levels. The cyclotides that continued to be expressed in suspension cultures shared similar sequence and biophysical properties as a group, regardless of phylogenetic origin of the host. Of particular interest was the discovery of inducibility by NaCl of cyclotide expression in O. affinis, cycloviolacin O2 expression in O. affinis, and the scale up of cycloviolacin O2 production in H. enneaspermus. Together the results presented here highlight the utility of plant cell suspensions as modalities to produce macrocyclic peptides.
Publisher: American Chemical Society (ACS)
Date: 23-03-2020
Publisher: Wiley
Date: 15-12-2016
DOI: 10.1111/NPH.13789
Abstract: Plants have evolved many strategies to protect themselves from attack, including peptide toxins that are ribosomally synthesized and thus adaptable directly by genetic polymorphisms. Certain toxins in Clitoria ternatea (butterfly pea) are cyclic cystine‐knot peptides of c . 30 residues, called cyclotides, which have co‐opted the plant's albumin‐1 gene family for their production. How butterfly pea albumin‐1 genes were commandeered and how these cyclotides are utilized in defence remain unclear. The role of cyclotides in host plant ecology and biotechnological applications requires exploration. We characterized the sequence ersity and expression dynamics of precursor and processing proteins implicated in butterfly pea cyclotide biosynthesis by expression profiling through RNA‐sequencing ( RNA ‐seq). Peptide‐enriched extracts from various organs were tested for activity against insect‐like membranes and the model nematode Caenorhabditis elegans . We found that the evolution and deployment of cyclotides involved their ersification to exhibit different chemical properties and expression between organs facing different defensive challenges. Cyclotide‐enriched fractions from soil‐contacting organs were effective at killing nematodes, whereas similar enriched fractions from aerial organs contained cyclotides that exhibited stronger interactions with insect‐like membrane lipids. Cyclotides are employed as versatile and combinatorial mediators of defence in C. ternatea and have specialized to affect different classes of attacking organisms.
Publisher: Springer Science and Business Media LLC
Date: 26-09-2014
Publisher: Elsevier BV
Date: 08-2022
Publisher: Elsevier BV
Date: 05-2020
Publisher: Public Library of Science (PLoS)
Date: 10-08-2011
Publisher: Elsevier
Date: 2015
Publisher: Wiley
Date: 23-07-2019
Publisher: Wiley
Date: 11-06-2016
DOI: 10.1111/PBI.12578
Publisher: Springer Science and Business Media LLC
Date: 12-02-2013
DOI: 10.1038/NCOMMS2450
Abstract: The production of adequate agricultural outputs to support the growing human population places great demands on agriculture, especially in light of ever-greater restrictions on input resources. Sorghum is a drought-adapted cereal capable of reliable production where other cereals fail, and thus represents a good candidate to address food security as agricultural inputs of water and arable land grow scarce. A long-standing issue with sorghum grain is that it has an inherently lower digestibility. Here we show that a low-frequency allele type in the starch metabolic gene, pullulanase, is associated with increased digestibility, regardless of genotypic background. We also provide evidence that the beneficial allele type is not associated with deleterious pleiotropic effects in the modern field environment. We argue that increasing the digestibility of an adapted crop is a viable way forward towards addressing food security while maximizing water and land-use efficiency.
Publisher: Springer Science and Business Media LLC
Date: 18-12-2015
DOI: 10.1038/NCOMMS10199
Abstract: Cyclotides are erse 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 Oa AEP1 b and find it functions preferably as a cyclase by coupling C-terminal cleavage of propeptide substrates with backbone cyclization. Interestingly, Oa AEP1 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 Oa AEP1 b is a powerful tool for use in peptide engineering applications where increased stability of peptide products is desired.
Publisher: Wiley
Date: 10-10-2012
Publisher: Cold Spring Harbor Laboratory
Date: 10-12-2021
DOI: 10.1101/2021.12.09.472022
Abstract: Plant molecular farming aims to provide a green, flexible, and rapid alternative to conventional recombinant expression systems, capable of producing complex biologics such as enzymes, vaccines, and antibodies. Historically, the recombinant expression of therapeutic peptides in plants has proven difficult, largely due to their small size and instability. However, some plant species harbour the capacity for peptide backbone cyclization, a feature inherent in stable therapeutic peptides. One obstacle to realizing the potential of plant-based therapeutic peptide production is the proteolysis of the precursor before it is matured into its final stabilized form. Here we demonstrate the rational domestication of Nicotiana benthamiana within two generations to endow this plant molecular farming host with an expanded repertoire of peptide sequence space. The in planta production of molecules including an insecticidal peptide, a prostate cancer therapeutic lead and an orally active analgesic are demonstrated.
Publisher: American Chemical Society (ACS)
Date: 26-04-2023
Publisher: Wiley
Date: 09-2010
Publisher: Springer Science and Business Media LLC
Date: 25-07-2019
DOI: 10.1038/S41598-019-47273-7
Abstract: Asparaginyl endopeptidases (AEPs) are a class of enzymes commonly associated with proteolysis in the maturation of seed storage proteins. However, a subset of AEPs work preferentially as peptide ligases, coupling release of a leaving group to formation of a new peptide bond. These “ligase-type” AEPs require only short recognition motifs to ligate a range of targets, making them useful tools in peptide and protein engineering for cyclisation of peptides or ligation of separate peptides into larger products. Here we report the recombinant expression, ligase activity and cyclisation kinetics of three new AEPs from the cyclotide producing plant Oldenlandia affinis with superior kinetics to the prototypical recombinant AEP ligase OaAEP1 b . These AEPs work preferentially as ligases at both acidic and neutral pH and we term them “canonical AEP ligases” to distinguish them from other AEPs where activity preferences shift according to pH. We show that these ligases intrinsically favour ligation over hydrolysis, are highly efficient at cyclising two unrelated peptides and are compatible with organic co-solvents. Finally, we demonstrate the broad scope of recombinant AEPs in biotechnology by the backbone cyclisation of an intrinsically disordered protein, the 25 kDa malarial vaccine candidate Plasmodium falciparum merozoite surface protein 2 (MSP2).
Start Date: 2020
End Date: 2023
Funder: Australian Research Council
View Funded ActivityStart Date: 2015
End Date: 12-2019
Amount: $659,100.00
Funder: Australian Research Council
View Funded ActivityStart Date: 12-2015
End Date: 12-2020
Amount: $2,977,310.00
Funder: Australian Research Council
View Funded ActivityStart Date: 02-2020
End Date: 02-2024
Amount: $652,000.00
Funder: Australian Research Council
View Funded Activity