BIOL3161: Genomics and its Applications (Convenor)
Our group has received four University medals, three outstanding honours theses awards and two awards for excellence in teaching and supervision in the past eight years (see below).
SIGNALING BETWEEN THE CHLOROPLAST AND NUCLEUS
The overarching theme of our research is to determine the controls and regulators of communication between the chloroplast and nucleus. This includes discovery of genes and metabolites involved in epigenetics, RNA metabolism, chloroplast-nuclear signaling, carotenoid biosynthesis, photosynthesis and drought.
program is an integral component of the ARC Centre of Excellence in Plant Energy Biology (see below). The Centre offers Honours scholarships ($6K) and topup scholarships for PhD students ($7K), in addition to well funded research, conference travel and graduate training programs. 1. Signaling during chloroplast development.
• First demonstration of a role for the cytoskeleton and a novel cytoskeleton-associated protein in chloroplast biogenesis (Albrecht et al 2010, Plant Cell).
• Elucidation of a mechanism for photosystem assembly that requires lipid vesicles and a protein disulphide isomerase that folds light harvesting and other photosystem proteins (Tanz et al. 2011, Plant Journal).
2. Identification of the first signal to move from the chloroplast to the nucleus
We are studying the mechanisms by which plants perceive and respond to drought and excess light. Recently, we uncovered a molecule that moves between the chloroplast and nucleus to regulate gene expression. The key publication is Estavillo et al 2011, Plant Cell, which builds upon Marin et al 2011 Plos One, Wilson et al. 2009 Plant J. and Rossel et al 2006.
3. Intersection of drought and high light signaling.
• Demonstration of a role for the ER and an ER processing protein in chloroplast-nuclear communication, specifically in response to drought (Che et al. 2010, Science Signaling)
• Commercial outputs. The knowledge of the SAL-PAP retrograde pathway has been published (Rossel et al. 2006, PCE Wilson et al. 2009, Plant Journal), patented and is being applied to the development of drought tolerant wheat in collaboration with CSIRO and GRDC and in Canola with Pacific Seeds via an ARC Linkage grant.
Also see Gonzalo Estavillo's web page.4. Epigenetic Regulation of Carotenoid Biosynthesis:
Carotenoids, such as beta-carotene, are essential for photosynthesis, dietary vitamin A and as antioxidants offer protection against certain cancers and age-related blindness. We made the first identification of an epigenetic regulator of carotenoid biosynthesis. Communication between the chloroplast and nucleus occurs in both directions and a seminal finding was the identification of a histone methylation transferase that regulates specific enzymes required for carotenoid biosynthesis, flowering time and hormone synthesis in the chloroplast. Future goals are to elucidate the epigenetic controls and identify novel carotenoid-derived retrograde signals produced from carotenoids that regulate nuclear gene expression and plant development. See Cazzonelli et al. 2009 Plant Cell and Cazzonelli web page 5. Leaf to leaf systemic signalling
A leaf exposed to full sunlight will transmit a signal to shaded leaves enable a systemic acquired acc
limation (SAA) response. The nature and regulation of SAA is under investigation.6. Photosynthesis and photoprotection
We are investigating the safety valves plants used to protect against oxidative damage induced during photosynthesis. This program is a combination of biochemical genetics and physiology using Arabidopsis and avocado.
7. Collaborative projects:
Several projects are undertaken by students based in CSIRO. For example, there is a project relating to cereal colour and nutritional content of wheat with Dr Crispen Howitt.
A key to our research is teamwork and applying cutting edge molecular and biochemical techniques in combination with whole plant physiology to build a picture from gene to crop.The approach utilizes deep sequencing, microarrays, promoter-reporter gene fusions, HPLC and GC-MS to identify novel genes and signalling pathways in Arabidopsis (related to Canola), wheat, avocado and canola. Some sample projects are listed below. More are available upon request. Also check out others in our group who have their own web sites.
Carotenoids and Plant Development
This proposal will unravel the regulatory mechanisms controlling carotenoid composition as well as plant growth.
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Understanding chloroplast/nuclear signaling and response pathways which determine photosynthetic capacity
Aim: To gain new insights into chloroplast/nuclear signaling pathways using in mutants where normal protein expression is perturbed by RNAi down regulation.
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The plant organelles responsible for the plants ability to perform photosynthesis, the chloroplasts, are essential for plant growth and vitality.
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Student research opportunities
Protein modification in chloroplast
A light sensitive mutant, snowy cotyledon 4, has been isolated with a mutation in a CAAX-proteinase function
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SCO Protein interaction partners
Several novel proteins have been identified in the mutant analysis of snowy cotyledon mutants, but mostly nothing is known about their function
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Gain of function mutants
In aim to unravel the regulatory network of chloroplast biogenesis second site mutants of snowy cotyledon 2 and snowy cotyledon 3 have been identified
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The generation of wheat cultivars with improved drought tolerance
Opportunities for students in this project
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- Veronica Albrecht (Visiting Fellow)
- Eng Kee Au (Honours Student)
- Andrew Bowerman (PhD student)
- Melanie Carmody (Visiting Fellow)
- Chris Cazzonelli (Divisional Visitor)
- Kai Chan (PhD student)
- Derek Collinge (Laboratory Manager)
- Peter Crisp (PhD student)
- Gonzalo Estavillo (Visiting Fellow)
- Diep Ganguly (PhD student)
- Diep Ganguly (Technical Assistant)
- Sophie Holland (Research Assistant)
- Xin Hou (PhD student)
- Nay Chi Khin (Honours Student)
- Nay Chi Khin (Lab Preparation)
- Nazia Nisar (Postdoctoral Scientist)
- Barry Osmond (Visiting Fellow)
- Samuel Perotti (Laboratory Technician)
- Su Yin Phua (PhD student)
- Barry Pogson (Lab Leader)
- John Rivers (PhD student)
- Tepsuda Rungrat (PhD student)
- Estee Tee (Administration Officer)
- Arun Yadav (Postdoctoral Scientist)
- Chun Wai (Ronald) Yu (PhD student)
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Lab awards and achievements
- Eleven "highly cited" articles have been in the top 1% of Plant and Animal Sciences with respect to ISI citations in past 10 years
- Two "hot" papers (top 0.1% of citations)
- Two articles recommended by Faculty of 1,000 (f1000.com)
- Chris Cazzonelli: Goldacre Medal, awarded by the Australian Society for Plant Physiology, 2010
- Kai Xun Chan: University Medal and India Australia Association Prize for the Most Outstanding Honours thesis in the College of Medicine, Biology and Environment Prize, 2010
- Xiao Hui Chew, Awarded the University medal, 2008 for an outstanding honours thesis
- Alexandra Chubb: Awarded the University medal and the ASBMB prize for an outstanding honours thesis, 2004
- Peter Crisp: India Australia Association Prize for the Most Outstanding Honours thesis in the College of Medicine, Biology and Environment Prize, 2009, Cold Spring Harbor Asia Fellowship Student Prize, 2011
- Abby Cuttriss: ASPS and Functional Plant Biology Best Paper Award for Young Scientists to Cuttriss et al. 2007
- Gonzalo Estavillo: ACT Tall Poppy Early Career Researcher Award, ALTC National Teaching Award, ASPS Teaching Award, Vice-Chancellors Excellence in Teaching Award, 2010-2011, Estavillo et al. 2011 selected by Editors for review in “In brief”
- Britta Förster: Rebiez Foundation Award for Best Paper in the area of Chloroplast Biology to Förster, Mathesius and Pogson, 2006
- Hyoungshin Park: Park et al Plant Cell selected by Editors for review in “In this Issue”, 2002
- Barry Pogson: Vice Chancellor’s Award for Excellence in Supervision of research students and postdoctoral fellows. One award is made annually at the ANU, 2005; Fenner Medal, awarded by the Australian Academy of Science for distinguished research in plant and animal sciences by scientists 40 years or under, 2001; Goldacre Medal, awarded by the Australian Society for Plant Physiology on the merit of original research by an early career scientist, 2000.
- Jan Bart Rossel: ARC APD Fellowship 2006, Cover of Plant Cell and Article selected by Editors for review in “In brief” for Rossel et al. 2007
- Philippa Walter: Awarded the ASBMB prize for an outstanding honours thesis, 2003
- Nick Woo: Awarded the University medal, 2005 for an outstanding Honours thesis
2011- 2013 Publications, 50 publications since 2008 (see link for complete list)
- Jung, H-S, Crisp, P, Estavillo, GM, Cole, B, Hong, F, Mockler, T, Pogson, BJ and Chory J (2013) A Subset of Heat Shock Transcription Factors Required for the Early Response of Arabidopsis to Excess Light. Proc. Natl. Acad. USA, online early doi:10.1073/pnas.1311632110.
- Albrecht-Borth, V, Fan, D, Collinge, D Marri, S, Kauss, D, Hu, Y, Liebers, M, Apel, K, Pfannschmidt, T Chow, WS, Pogson, BJ (2013) A novel proteinase, SCO4, is required for photosynthetic acclimation to higher light intensities in Arabidopsis. Plant Physiology, online early doi:10.1104/pp.113.216036.
- Cazzonelli, CI, Vanstraelen, M, Yin, K Carron-Arthur, A, Nisar, N, Tarle, G, Cuttriss, AJ, Searle, IS, Simon, S, Benkova, E, Mathesius, U, Masle, J, Friml, J, and Pogson, BJ (2013) Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS ONE 8(7):e70069.
- Estavillo, GM, Verhertbruggen, Y, Pogson, BJ, Heazlewood, J, Scheller, HV and Ito, J (2013) Isolation of the plant cytosolic fraction for proteomic analysis. Methods in Molecular Biology (In press).
- Caliandro, R, Nagel, KA, Kastenholz, B, Bassi, R Li, Z, Niyogi, KK, Pogson, BJ, Schurr U and Matsubura, S (2013) Effects of altered α- and β-branch carotenoid biosynthesis on photoprotection and whole-plant acclimation of Arabidopsis to photo-oxidative stress. Plant, Cell & Environment 36:438-453
- Carmody, M and Pogson, BJ (2013) Systemic photo-oxidative stress signaling. IN Long-Distance Systemic Signaling and Communication in Plants. Ed F. Baluska, Springer, Dordrecht pp 251-274.
- Pogson BJ and Albrecht, V (2012) An overview of chloroplast biogenesis and development. IN Plastid Biology, Eds SM Theg and F-A Wollman, Advances in Plant Biology, Springer (in press).
- Nisar, N, Verma, S, Pogson, BJ and Cazzonelli, CI (2013) Inflorescence stem grafting made easy in Arabidopsis. Plant Methods 8:50.
- Husen, J, Förster, B, Chow, WS, Pogson, BJ and Osmond, CB (2013) Decreased photochemical efficiency of Photosystem II following sunlight exposure of shade-grown leaves of avocado (Persea americana Mill.): because of, or in spite of, two kinetically distinct xanthophyll cycles? Plant Physiology 161:836-852 doi:10.1104/pp.112.209692.
- Chan, KX, Wirtz, M, Phua, SY, Estavillo, GM and Pogson, BJ (2013) Balancing metabolites in drought: the sulfur assimilation conundrum. Trends in Plant Science 18:18-29.
- Gordon, MJ, Carmody, ME, Albrecht, V and Pogson, BJ (2012) Systemic and local responses to repeated HL stress-induced retrograde signaling in Arabidopsis. Frontiers in Plant Physiology 3:303 doi: 10.3389/fpls.2012.00303.
- Estavillo, GM, Chan, KX, Phua, SY and Pogson, BJ (2012) Reconsidering the nature and mode of action of metabolite retrograde signals from the chloroplast. Frontiers in Plant Physiology 3:300 doi: 10.3389/fpls.2012.00300
- Matsubara, S, Förster, B, Waterman, M, Robinson, SA, Pogson, BJ, Gunning, B and Osmond, CB (2012) From ecophysiology to phenomics: some implications of photoprotection and shade-sun acclimation in situ for dynamics of thylakoids in vitro. Phil. Transactions Royal Society B doi:10.1098/rstb.2012.0072
- Zhang, B, Carrie, C, Ivanova, A, Narsai, R, Murcha, MW, Duncan, O, Wang, Y, Law, SR, Albrecht, V, Pogson, BJ, Giraud, E, van Aken, O and Whelan J (2012) LETM proteins play a role in the accumulation of mitochondrially encoded proteins in Arabidopsis thaliana and AtLETM2 displays parent of origin effects. J. Biol. Chem. jbc.M112.383836. First Published on October 5, 2012, doi:10.1074/jbc.M112.383836
- Gruissem, W, Lee, C-H, Oliver, M and Pogson, B (2012) The Global Plant Council: Increasing the impact of plant research to meet global challenges. J. Plant Biol. 55: 343-348.
- Williams, M, Lean, M, Pogson, B and Martin, C (2012) Plants, food and human health: You are what you eat? Plant Cell 24 (4) tpc.112.tt0412
- Nichol, CJ, Pieruschka, R, Takayama, K, Förster, B, Kolber, Z, Rascher, U, Grace, J, Robinson, SA, Pogson, BJ, and Osmond, CB (2012) Canopy conundrums: exploring the envelope of reversible down-regulation of photosynthesis in the outer and inner canopy to scale observations from the leaf to the landscape. Functional Plant Biology 39:1-24.
- Tanz, SK, Kilian, J, Johnsson, C, Apel, K, Small, ID, Harter, K, Wanke, K, Pogson, BJ and Albrecht, V (2012) The SCO2 protein disulphide isomerase is required for thylakoid biogenesis and interacts with LCHB1 chlorophyll a/b binding proteins which affects chlorophyll biosynthesis in Arabidopsis seedlings. Plant Journal 69: 743-54. (featured article and cover)
select earlier publications
- Estavillo, GM, Crisp, PA, Pornsiriwong, W, Wirtz, M, Collinge, D, Carrie, C, Giraud, E, Whelan, J, David, P, Javot, H, Brearley, C, Hell, R, Marin, E and Pogson, BJ (2011) Evidence for a SAL1-PAP Chloroplast Retrograde Pathway that Functions in Drought and High Light Signaling in Arabidopsis. Plant Cell 23: 3992-4012
- Cuttriss, AJ, Cazzonelli, CI, Wurtzel, ET and Pogson, BJ (2011) Vitamin A (carotenoids). IN Biosynthesis of vitamins in Plants, Eds F. Rébeillé and R. Douce, Advances in Botanical Research
- Hirsch J, Misson J, Crisp PA, David P, Bayle V, Estavillo GM, Javot H, Chiarenza S, Mallory AC, Maizel A, Declerck M, Pogson BJ, Vaucheret H, Crespi M, Desnos T, Thibaud M-C, Nussaume L, Marin E (2011) A Novel fry1 Allele Reveals the Existence of a Mutant Phenotype Unrelated to 5'->3' Exoribonuclease (XRN) Activities in Arabidopsis thaliana Roots. PLoS ONE 6(2): e16724
- Förster, B, Pogson, BJ and Osmond CB (2011) Lutein from de-epoxidation of lutein epoxide replaces zeaxanthin to sustain an enhanced capacity for non-photochemical chlorophyll fluorescence quenching in avocado shade leaves in the dark. Plant Physiol. 156: 393-403.
- Pogson, BJ, and Albrecht, V (2011) Genetic dissection of chloroplast biogenesis and development: an overview. Plant Physiol. 155:1545-1551.
- *Woo, NS, *Gordon, MJ, Graham, SR, Rossel, JB, Badger, MR and Pogson, BJ (2011) A mutation in the purine biosynthetic enzyme ATASE2 impacts high light signalling and acclimation responses in green and chlorotic sectors of Arabidopsis leaves. Functional Plant Biology 38:401-419.
- Albrecht V, Estavillo GM, Cuttriss AJ and Pogson BJ (2011) Identifying chloroplast biogenesis and signalling mutants in Arabidopsis thaliana. Methods in Molecular Biology 684:257-72.
- Albrecht, V, Šimková, K, Carrie, C, Delannoy, E, Giraud, E Whelan, J, Small, I Apel, K, Badger, M and Pogson, BJ (2010) The cytoskeleton and the peroxisomal-targeted SNOWY COTYLEDON 3 protein are required for chloroplast development in Arabidopsis. Plant Cell 22(10):3423-38.
- Che, P, Bussell, JD Zhou, W Estavillo, G, Pogson, BJ, Smith SM (2010) Signaling from the Endoplasmic Reticulum Activates Brassinosteroid Signaling and Promotes Acclimation to Stress in Arabidopsis. Science Signaling 3 (141), ra69. [DOI: 10.1126/scisignal.2001140].
- Cazzonelli CI and Pogson BJ. (2010) A balance between source and sink: regulation of carotenoid composition in plants. Trends in Plant Science 15(5): 266-274
- Cazzonelli, CI, Cuttriss, AJ, Cossetto, SB, Pye, W, Whelan, J, Finnegan, J, Turnbull, C and Pogson, BJ (2009) Epigenetic regulation of carotenoid composition in Arabidopsis. Plant Cell 21: 39-53.
- Wilson, PB, Estavillo, GM, Field, KJ, Carroll, AJ, Pornsiriwong, W, Howell, KA, Lake, JA, Millar, AH, von Caemmerer, S, Pogson, BJ (2009) The nucleotidase/phosphatase, SAL1, is a negative regulator of drought tolerance in Arabidopsis. Plant Journal 58: 299-317
- Delannoy, E, Le Ret, M, Faivre-Nitschke, SE, Estavillo, GM, Bergdoll, M, Taylor, NL, Pogson, BJ, Small, ID, Imbault, P, and Gualberto, JM (2009) Arabidopsis tRNA adenosine deaminase (TADA) is responsible for editing the wobble nucleotide of chloroplast tRNAArg(ACG), a modification essential for efficient chloroplast translation. Plant Cell 21: 2058-2071
- Millar, AH, Carrie, C, Pogson, BJ and Whelan J (2009) Exploring the function:location nexus - using multiple lines of evidence in defining the subcellular location of plant proteins Plant Cell 21: 1625-1631.
- Rossel, JB Wilson, PB, Hussain, D, Woo, NS, Gordon, MJ, Mewett, OP, Howell, KA, Whelan, J, Kazan, K, Pogson, BJ (2007) Systemic and Intracellular Response to Photooxidative stress in Arabidopsis Plant Cell 19: 4091-4110. (ISI highly cited)
- Pogson, B.J., Woo, NS, Förster B and Small, ID (2008) Plastid signalling to the nucleus and beyond. Trends in Plant Science 13 (11): 602-609 (ISI highly cited)
- DellaPenna, D. and Pogson, B.J. (2006) Vitamin synthesis in plants: tocopherols and carotenoids. Annual Review of Plant Biology 57: 711-738 (ISI highly cited)
- Millgate, A.G., Pogson, B.J., Wilson, I.W., Zenk, M.H., Gerlach, W.L., Fist, A.J. and Larkin, P.J. (2004) A morphine-free mutant of opium poppy - changing the poppy analgesic industry. Nature 431:413-414.
- Park H., Kreunen S.S., Cuttriss, A.J., DellaPenna, D., Pogson B.J. (2002) Identification of the carotenoid isomerase provides insight into carotenoid biosynthesis, prolamellar body formation and photomorphogenesis. Plant Cell 14: 321-332. (ISI highly cited)
- Pogson B.J., Niyogi K.K., Björkman O., and DellaPenna D. (1998) Altered xanthophyll compositions adversely affect chlorophyll accumulation and nonphotochemical quenching in Arabidopsis mutants. Proc. Natl. Acad. Sci. USA 95: 13324-29.
- Pogson B.J., McDonald K., Truong M., Britton G., and DellaPenna D. (1996) Arabidopsis carotenoid mutants demonstrate lutein is not essential for photosynthesis in higher plants. Plant Cell 8: 1627-1639.
Click here to see a full list of publications on the ISI website...
- Cazzonelli and Pogson. “The hunt for Ribonucleic Acid riboswitches and genetic sensors of metabolic flux in plants" $375K
- Foley, Carroll, Badger, Pogson et al. “High-throughput sample preparation robotics to enable emerging large-scale plant genomics, metabolomics and proteomics research” ARC LIEF $280KBadger, Von Caemmerer, Price, Goodnow, Pogson “Improving plant productivity and human health using next generation biotechnology approaches” ARC SuperScience Fellowships $556.8K
- Borevitz, Von Caemmerer, Balasubramanian, Millar, Small, Pogson et al “Spectral climate chamber facilities for phenomic studies of plant light response adaptation” ARC LIEF $500K
- Pogson, Estavillo and Howitt “The generation of wheat cultivars with improved drought tolerance and agronomic traits” Grains Research Development Council $300K
- Pogson, Easton, A “Towards improving the yield of canola and other brassicas during drought”, ARC Linkage $240K
- Whelan, Smith, Badger, Small, Millar, Day, Pogson, "ARC Centre of Excellence in Plant Energy Biology (CPEB)", $2.5M per annum.
The ARC Centre of Excellence in Plant Energy Biology
is a group of students, postdocs, research asstiants and chief investigators at ANU, University of Western Australia and Flinders University. The Chief Investigators are Badger, Day, Millar, Pogson, Small, Tyerman and Whelan. The Centre offers Honours scholarships ($6K) and topup scholarships for PhD students ($7K), in addition to well funded research, conference travel and graduate training programs.
for more details, news and research opportunities.
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