Doctor Chris Cazzonelli


Dr Chris Cazzonelli Dr Christopher Cazzonelli completed his Bachelor of Science (Honours Class I) at the University of Queensland. Next he won an Australian Postgraduate Award to study plant molecular biology and plant genetic engineering under the supervision of Prof. Jimmy Botella. Dr. Cazzonelli enhanced knowledge of mechanosensitive (touch) gene regulation and completed his PhD at the University of Queensland in 2002.

He subsequently won a prestigious United States Department of Agriculture Postdoctoral Fellowship to work with Dr. Jeff Velten (USDA-ARS, Cropping Systems Research Laboratory, USA) and investigate the molecular nature of gene activation, gene silencing and remote sensing of plant stress events.

In 2006, Dr. Cazzonelli was recruited by the ARC Centre of Excellence in Plant Energy Biology (Australian National University) to work with Prof. Barry Pogson and investigate what regulates the production of health promoting secondary metabolites in plants.

Dr. Cazzonelli lead a team to discover epigenetic regulatory mechanisms controlling carotenoid accumulation as well as plant development, and established a new wave in carotenoid regulatory biology that won him the prestigious Goldacre Medal in 2010.

Dr. Cazzonelli now joins Western Sydney University, Hawkesbury Institute for the Environment as a Senior Lecturer in Plant Molecular Biology. He is establishing an Environmental Epigenetics Laboratory (EEL) and team of researchers to discover molecular mechanisms underpinning plant acclimation and adaptation to changing environments (e.g. temperature, elevated CO2, mechanical stimulation and drought).

A multidisciplinary approach is being undertaken to investigate how RNA secondary structure and epigenetic modifications regulate metabolite accumulation and ultimately promote memory-forming processes in model plants, crops and native forest species.

Environmental Epigenetic Laboratory Overview

Current Research Projects and Student Opportunities

Value Adding in Plants

The ultimate aim of the Environmental Epigenetics Laboratory is to understand how changes in the environment (e.g. rising temperatures, higher CO2 levels, drought and mechanical stress) influence regulatory mechanisms and metabolite accumulation in plants, processes that can facilitate memory, cellular acclimation, reproduction and plant adaptation.

Research projects span across disciplines, from genome to phenotype. Projects offer experience in a range of next generation sequencing, molecular, genetic, epigenetic, metabolic, transgenic, genetic engineering, phenomic and reporter gene technologies.

The goal is to develop new solutions that can improve plant performance and facilitate agricultural sustainability. Model plant species (Arabidopsis, tobacco and tomato) and agronomic important crops (e.g. cotton and peanut) will be used to answer fundamental scientific questions and address key hypotheses relating to cutting edge research topics.

Honours and PhD research projects are available for qualified, enthusiastic and talented postgraduate students. Mentored science research projects are also available to undergraduate students and summer scholars. Post-doctoral research candidates are also invited to contact me with regard to potential research projects and funding opportunities.

1. The Hunt for RNA Riboswitches that regulate plant metabolism and contribute to memory forming epigenetic events.

Bacteria and plants are natural chemical factories producing nutrient metabolites such as Vitamin B (e.g. thiamine) and antioxidant pigments (e.g. carotenoids). These metabolites are essential for human health, plant energy and facilitate cellular communications by controlling their own biosynthesis within energy organelles. They can do this by altering the packaging and structure of genetic material within the nucleus, which controls gene expression.

The structure of Ribonucleic Acid (RNA) can influence the molecular nature of gene expression by controlling transcription attenuation, translation initiation, mRNA splicing and mRNA processing. In bacteria, ancient RNA structural switches (called riboswitches) sense metabolite (ligand) concentrations and control gene expression or protein levels. They are widespread identified in bacteria, animals and one in plants.

This ARC funded project aims to; 1) identify RNA switches in plants that control secondary metabolism, and 2) demonstrate how changes in temperature alter RNA structure and gene regulation in Arabidopsis, and 3) link metabolite production to DNA memory forming processes that facilitate cellular adaptation.

2. The discovery of how phytochemical variation and environmental stress affects plant development and biotic interactions within the rhizosphere.

Carotenoid Pathway

Changing environmental conditions (rising temperatures and CO2 in combination with water availability) can affect the temporal and spatial variation of plant secondary metabolite profiles of pharmaceutically and nutritionally important plants. The accumulation of secondary metabolites in the rhizosphere (zone of soil surrounding plant roots) can affect microbial and mycorrhizal associations that promote nutrient uptake and essentially enhance plant growth.

Carotenoids for example are colourful pigments found in plants that are essential for human health. In plants, carotenoids are required for photosynthesis, photoprotection and the production of signaling molecules (e.g. hormones and volatiles) that promote chloroplast to nucleus communication, shoot branching, root-mycorrhizal symbiosis, parasitic weed germination and abiotic stress resistance (Cazzonelli and Pogson, Trends in Plant Science 2010; 15: 266-274).

We have shown that alterations in carotenogenesis and hence the synthesis of carotenoid-derived signaling molecules can perturb root and shoot development (Cazzonelli et al., Plant Cell 2009; 21,39-53: Van Norman, et al., PNAS 2014; In Press).

This project aims to; 1) investigate how perturbations in metabolite profiles influence root development, and 2) establish links between temperature change, development and the regulation of secondary metabolism, 3) assess gene expression and phytochemical profiles of genetic diverse plant populations growing under variable soil microenvironments, and 4) identify signaling molecules essential for promoting a healthy soil microenvironment and maintaining agricultural sustainability.

3. An epigenetic investigation into the phenomenon of thigomorphogenesis in plants?


Plants sense and respond to wind, rubbing, insect feeding, touching and mechanical stress by altering their phenotype, a phenomenon called thigmomorphogenesis. This is the physiological and morphological adaptation by a plant to environmental mechanical influences.

Changes can include less elongation, thicker stems, enhanced senescence, delayed flowering, altered leaf morphology, enhanced pest resistance and decreased susceptibility to various stresses. The altered growth responses associated with mechanical stress can decrease photosynthesis and are also coupled to increases in respiration.

Despite the widespread relevance of thigmomorphogenesis, the molecular nature that underlies plant mechanostimulus-induced morphological responses remains rather enigmatic and largely unknown. Recent evidence in our laboratory shows that chromatin modifications regulate mechanical induced gene expression.

The project will address the following questions; 1) what are the regulatory mechanisms controlling mechanical touch induced gene expression, 2) how do chromatin modifications target gene loci, 3) does mechanical-induced growth responses involve epigenetic memory formation, and 4) is thigomomorphogenesis a process of cellular acclimation or plant adaptation?

Dr Rishi Aryal

Dr Rishi Aryal

ResearchGate Email
Eric Brenya

Eric Brenya

ResearchGate Email
Namraj Dhami

Namraj Dhami

ResearchGate Email

Postdoctoral Research Associates

Dr Rishi Aryal

Current Postgraduate Students

  • 2016 Yagiz Alagoz; PhD (Regulation of the untranslated mRNA leader sequence in response to environmental, metabolic and epigenetic perturbations in plants, UWS-HIE)
  • 2015 Eric Brenya; PhD (Elucidating thigmomorphogenesis: An epigenetic phenomenon of plant stress acclimation and transgenerational adaptation, UWS-HIE) 
  • 2015 Namraj Dhami; PhD (Environmental regulation of nutritional and medicinal metabolite accumulation in plants, UWS-HIE)
  • 2014 John Rivers; PhD (RNA secondary structure and its effect upon gene expression in plants; co-supervised with Prof. Barry Pogson, Australian National University)
  • 2012 Xin Hou; PhD (Hunting for genes that link cis-carotenes to chloroplast development; co-supervised with Prof. Barry Pogson, Australian National University)

Current Undergraduate Students

  • 2016 Grace Scott (300910/Advanced Science Project C and 300913/Field Project 1;  Biofortification of Tomato: Investigating novel roles for carotenoids in mutualistic mycorrhiza associations)
  • 2015 Wendy Ng (HIE Summer Scholar: Characterisation of an Arabidopsis carotenoid mutant with an altered root phenotype)
  • 2014 Inan Muhsin (UWS Science Research Project: Investigating carotenoid regulatory pathways using a suppressor mutant screen)

Past Postgraduate Students

  • 2013 Sophie Holland (Honours: The molecular nature of metabolic feedback regulation in plants)
  • 2012 Jacinta Watkins (Honours: cis-carotenes: Do they have regulatory roles in plants)
  • 2010 Alice Burgess (Honours: Investigating the role and function of the chromatin modifying protein, SDG8 in plant development)
  • 2009 Andrea Roberts (Honours: Characterisation of the histone methyltransferase SET DOMAIN GROUP 8, in Arabidopsis thaliana).
  • 2007 Melanie Carmody (Honours: Characterisation of the CRTISO Promoter).

Selected Publications

Book Chapters

Baranski R and Cazzonelli CI (2015) 'Carotenoid biosynthesis and regulation in plants'. In Carotenoids: Nutrition, Analysis and Technology (A. Kaczor and M. Baranska), pp 159-189, John Wiley & Sons, Ltd, Oxford

Cuttriss AJ, Cazzonelli CI, Wurtzel ET, Pogson BJ, (2011) 'Carotenoids', In Biosynthesis of Vitamins in Plants, Advances in Botanical Research, vol58. Ed. Rébeillé, F. and Douce, R. Elsevier, Amsterdam, The Netherlands, pp 1-36

Cazzonelli CI, Nisar N, Hussain D, Carmody M, Pogson BJ, (2010) 'Biosynthesis and Regulation of Carotenoids in Plants- micronutrients, vitamins and health benefits', In Plant Developmental Biology-Biotechnology Perspectives, vol.2, Ed. E.C. Pua and M.R. Davey Springer-Verlag Berlin Heidelberg, pp 117-137

Journal Articles

Zhang B, Aken OV, Thatcher L, Clercq ID, Duncan O, Law SR, Murcha MW, van der Merwe M, Seifi HS, Carrie C, Cazzonelli CI, Radomiljac J, Höfte M, Singh KB, Breusegem FV, Whelan J, (2014) 'The mitochondrial outer membrane AAA ATPase AtOM66 affects cell death and pathogen resistance in Arabidopsis thaliana', Plant Journal, (in press) 

Avendano-Vazquez AO, Cordoba E, Llamas E, San Roman C, Nisar N, De la Torre S, Ramos-Vega M, Gutierrez-Nava MD, Cazzonelli CI, Pogson BJ, Leon P, (2014) 'An Uncharacterized Apocarotenoid-Derived Signal Generated in zeta-Carotene Desaturase Mutants Regulates Leaf Development and the Expression of Chloroplast and Nuclear Genes in Arabidopsis', Plant Cell, vol.26, no.6, pp 2524-2537

Cazzonelli CI, Nisar N, Roberts AC, Murray KD, Borevitz JO, Pogson BJ, (2014) 'A chromatin modifying enzyme, SDG8, is involved in morphological, gene expression, and epigenetic responses to mechanical stimulation', Frontiers in Plant Science, vol.5, Article no.533

Nisar N, Cuttriss AJ, Pogson BJ, Cazzonelli CI, (2014) 'The promoter of the Arabidopsis PIN6 auxin transporter enabled strong expression in the vasculature of roots, leaves, floral stems and reproductive organs' (opens in a new window), Plant Signaling & Behavior,vol.9, no.1, e27898

Van Norman JM, Zhang J, Cazzonelli CI, Pogson BJ, Harrison PJ, Bugg TD, Chan KX, Thompson AJ, Benfey PN, (2014) 'Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative' (opens in a new window), Proceedings ot the National Academy of Sciences of the USA, vol.111, no.13, pp E1300-E1309

Cazzonelli CI, Vanstraelen M, Simon S, Yin K, Carron-Arthur A, Mathesius U, Cuttriss AJ, Tarle G, Searle I, Masle J, Benkova E, Friml J, Pogson BJ, (2013) 'Role Of The Arabidopsis PIN6 Auxin Transporter In Auxin Homeostasis And Auxin-Mediated Development' (opens in a new window), PLoS One, vol.8, no.7, article no.e70069

Velten J, Cakir C, Youn E, Chen J, Cazzonelli CI, (2012) 'Transgene Silencing and Transgene-derived siRNA Production in Tobacco Plants Homozygous for an Introduced AtMYB90 Construct' (opens in a new window), PLoS One, vol.7, no.2, article no.e30141

Cazzonelli CI, (2011) 'Carotenoids in Nature: insights from plants and beyond' (opens in a new window), Functional Plant Biology, vol.38, pp 833–847

Cazzonelli CI, Pogson BJ, (2010) 'Source and Sink: regulation of carotenoid composition in plants', Trends in Plant Science, vol.15, no.5, pp 266-274

Cazzonelli CI, Roberts A, Carmody M, Pogson BJ, (2010) 'Transcriptional Control of SET DOMAIN GROUP8 and CAROTENOID ISOMERASE during Arabidopsis Development' (opens in a new window), Molecular Plant, vol.3, no.1, pp 174-191

Velten J, Chakir C, Cazzonelli CI, (2010) 'A spontaneous dominant-negative mutation within a 35S::AtMYB90 transgene inhibits flower pigment production in tobacco' (opens in a new window), PLoS One, vol.5, no.3, article no. e9917

Wever W, McCallum EJ, Chakravorty D, Cazzonelli CI, Botella JR, (2010) 'The 5 ′ untranslated region of the VR-ACS1 mRNA acts as a strong translational enhancer in plants' (opens in a new window), Transgenic Research, vol.19, no.4, pp 667-674

Cazzonelli CI, Cuttriss AJ, Cossetto SB, Pye W, Crisp P, Whelan J, Finnegan J, Turnbull C, Pogson BJ, (2009) 'Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8' (opens in a new window), Plant Cell, vol.21, no.1, pp 39-53

Cazzonelli CI, Millar T, Finnegan J, Pogson BJ, (2009) 'Promoting gene expression in plants by permissive histone lysine methylation' (opens in a new window), Plant Signaling & Behavior, vol.4, no.6, pp 484-488

Cazzonelli CI, Yin K, Pogson BJ, (2009) 'Potential implications for epigenetic regulation of carotenoid biosynthesis during root and shoot development' (opens in a new window), Plant Signaling & Behavior, vol.4, no.4, pp 339-341

Howitt CA, Cavanagh C, Bowerman AF, Cazzonelli CI, Rampling L, Mimica JL, Pogson BJ, (2009) 'Alternative splicing, activation of cryptic exons and amino acid substitutions in carotenoid biosynthetic genes are associated with lutein accumulation in wheat endosperm' (opens in a new window), Functional and Integrative Genomics, vol.9, pp 363-373

Cazzonelli CI, Velten JP, (2008) 'In vivo characterisation of plant promoter element interaction using synthetic promoters' (opens in a new window), Transgenic Research, vol.17, pp 437–457

Cazzonelli CI, Velten JP, (2006) 'An in vivo luciferase-based transient assay system using Agrobacteria-infiltrated tobacco leaves: implications for post-transcriptional gene silencing' (opens in a new window), Planta, vol.224, pp 582-597

Cazzonelli CI, Burke J, Velten JP, (2005) 'Functional characterization of the geminiviral conserved late element (CLE) in uninfected tobacco', Plant Molecular Biology, vol.58, no.4), pp 465-481

Cazzonelli CI, McCallum E, Lee, R, Botella JR, (2005) 'Characterisation of a strong, constitutive mung bean (Vigna radiata L.) promoter with a complex mode of regulation in planta', Transgenic Research, vol.14, pp 941-967

Velten JP, Morey K, Cazzonelli CI, (2005) 'Plant viral intergenic DNA sequence repeats with transcriptional enhancing activity', Virology Journal, vol.2, no.1, p 16


Cazzonelli CI and Botella JR (1998). Patent Application No. PP5572/98 "A Novel Plant Promoter and Uses Therefor" The present invention provides a plant promoter capable of induction by physical and/or environmental stimuli in cells in which the promoter is indigenous and, in the absence of any negative regulatory mechanism, is capable of constitutive expression in cells in which the promoter is non-indigenous.

The invention is further directed to derivatives of the subject promoter including modular forms of the promoter which are, for example, inducible by different physical and environmental stimuli or which are constitutively expressed. The promoter of the present invention has a range of uses including directing expression of genes conferring useful traits on plants. UniQuest Pty Limited, University of Queensland, Brisbane, Australia

Grants / Current Projects

  • 2013-ARC Discovery Grant (DP130102593; $375,000). The Hunt for RNA Riboswitches and Genetic Sensors of Metabolic Flux in Plants. Cazzonelli CI (Lead Investigator), Pogson BJ, Aharoni, A.
  • 2008-ARC Linkage Infrastructure, Equipment and Facilities ($550,000). A massively parallel genome analysis facility for the ACT region (LE0989589).

Areas Of Research

  • Molecular biology
  • genomics
  • epigenetics
  • RNA regulation
  • riboswitches
  • secondary metabolism
  • carotenoids
  • anthocyanin
  • chlorophyll
  • plant energy biology
  • organelle signalling
  • cellular communication
  • genetic engineering
  • crop biofortication
  • environmental stress regulation
  • plant acclimation and adaptation
  • Curcumin
  • Thermoswitch
  • Tomato
  • Arabidopsis
  • Turmeric
To discuss opportunities within the Epigenetics and Plant Molecular Biology field, please contact me on (02) 4570 1752 or by email on

The EEL team enjoys the nature of spring and welcomes PhD candidate Yagiz Alagoz as well as HIE internship awardee Jordan Hollis (left to right: Jordan Hollis, Dr Rishi Aryal, Mr Eric Brenya, Mr Namraj Dhami, Mr Yagiz Alagoz and Dr Chris Cazzonelli).

Epigenetics in Nature: EELab First Christmas Party 2015 with Rishi Aryal, Namraj Dhami, Eric Brenya and Chris Cazzonelli at a secret location in the Kurrajong Heights

The EEL team continues to grow and welcomes new PhD candidate Namraj Dhami and HIE internship awardee Tracey Azzopardi (left to right: Ms Tracey Azzopardi, Dr Rishi Aryal, Mr Namraj Dhami and Dr Chris Cazzonelli).

Awards & Recognition

» 2010 Peter Goldacre Medal from the Australian Society of Plant Scientists (awarded yearly to an early career researcher for their outstanding contribution to Plant Science within 10 years of their PhD)

» 2003-05 Outstanding Performance Certificates of Merit (United States Department of Agriculture)

» 2001-03 USDA-ARS Post-Doctoral Fellowship

» 1996-99 Australian Postgraduate Award

Epigenetics Research

Eucalyptus Leaf