Professor Barry Pogson

Group Leader, Pogson Group - Chloroplast to nuclear signalling: light, drought and carotenoids
Barry Pogson completed his PhD at Macquarie University. He moved to the USA in 1994 working as a postdoc with Dean DellaPenna before taking an Assistant Professorship at Arizona State University in 1997. He moved to ANU late 1999. Pogson is Deputy Director of the ARC Centre of Excellence in Plant Energy Biology (www.plantenergy.edu.au) and lead CI on an International Wheat Yield Partnership grant to Improve Wheat Yeild by Optimising Energy Use Efficiency (iwyp.org). Notable acheivements and roles in the science community include:

Research interests

The focus of our research is to understand signaling between the chloroplast and nucleus during development, drought and high light stress..  This includes discovery of proteins involved in epigenetics, RNA metabolism, chloroplast-nuclear signalling, carotenoid biosynthesis, photosynthesis and drought. 

Our strategy is to apply cutting edge molecular and biochemical techniques in combination with whole plant physiology to build a picture from gene to crop.The approach utilizes a range of technologies from next generation  sequencing to HPLC and GC-MS to identify novel genes and signalling pathways in model plants and crops.

The research program is an integral component of the ARC Centre of Excellence in Plant Energy Biology (see below). The Centre offers Honours scholarships and topup scholarships for PhD students, in addition to well funded research, conference travel and graduate training programs.

1.  Chloroplast retrograde signalling and Drought. We are studying the mechanisms by which plants perceive and respond to drought and excess light. This requires signals from the chloroplast to the nucleus, a process known as retrograde signaling. We have uncovered a molecular that moves between the two organelles to regulate gene expression and are investigating its function in Arabidopsis. We are applying this knowledge to the development of drought tolerant wheat.

2. Carotenoid dervitaives as retrograde signals in plant development and acclimation to stress

Our work is focused on the characterization of plant pigments, particularly carotenoids and their role in photosynthesis and chloroplast development. Carotenoids are important pigments in photosystems, many fruits, flowers, and seafood. Nutritionally they are the source of vitamin A and offer some protection against certain cancers, heart and eye diseases. Thus, understanding their biosynthesis may lead to improved nutritional value of foods. The goals are to elucidate the mechanisms that control carotenoid accumulation using biochemical genetics. 

Novel carotenoid cleavage products, yet to be identified, impact diverse processes in plants. What they are and how they function is under investigation.

3. Leaf to leaf systemic signalling A leaf exposed to full sunlight will transmit a signal to shaded leaves enable a systemic acquired acclimation (SAA) response. The nature and regulation of SAA is under investigation.

4. Optimising Energy Use Efficiency: A goal of the ARC Centre of Excellence and our IWYP grant on wheat is to determing the constraints on energy capture and use by a cell, then select for crops and identify the underlying genes that will improve energy use efficiency and thus yield.

5. Collaborative projects: Several projects are undertaken by students based in CSIRO and at other nodes of the ACR Centre of Excellence

Morec details on our projects are available upon request.

  • Watkins, J & Pogson, B 2020, 'Prospects for Carotenoid Biofortification Targeting Retention and Catabolism', Trends in Plant Science, vol. 25, no. 5, pp. 501-512.
  • Ahmad Rashid, F, Crisp, P, Zhang, Y et al. 2020, 'Molecular and physiological responses during thermal acclimation of leaf photosynthesis and respiration in rice', Plant Cell and Environment, vol. 43, no. 3, pp. 594-610.
  • Watkins, J, Li, M, McQuinn, R et al. 2019, 'A GDSL Esterase/Lipase Catalyzes the Esterification of Lutein in Bread Wheat', The Plant Cell, vol. 31, no. 12, pp. 3092-3112.
  • Zhao, C, Wang, Y, Chan, K et al 2019, 'Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 11, pp. 5015-5020.
  • Rungrat, T, Almonte, A, Cheng, R et al 2019, 'A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana', Plant Direct, vol. 3, no. 5, pp. 1-13.
  • Rivers, J, Truong, T, Pogson, B et al 2019, 'Volatile apocarotenoid discovery and quantification in Arabidopsis thaliana: optimized sensitive analysis via HS-SPME-GC/MS', Metabolomics, vol. 15, no. 79, pp. 1-13.
  • Osmond, C, Chow, W, Pogson, B et al 2019, 'Probing functional and optical cross-sections of PSII in leaves during state transitions using fast repetition rate light induced fluorescence transients', Functional Plant Biology, vol. 46, no. 6, pp. 567-583.
  • Coast, O, Shah, S, Ivakov, A et al 2019, 'Predicting dark respiration rates of wheat leaves from hyperspectral reflectance', Plant Cell and Environment, vol. 42, no. 7, pp. 2133-2150.
  • Eriksson, D, Kershen, D, Nepomuceno, A et al 2019, 'A comparison of the EU regulatory approach to directed mutagenesis with that of other jurisdictions, consequences for international trade and potential steps forward', New Phytologist, vol. 222, no. 4, pp. 1673-1684.
  • Yadav, A, Carroll, A, Estavillo, G et al. 2019, 'Wheat drought tolerance in the field is predicted by amino acid responses to glasshouse-imposed drought', Journal of Experimental Botany, vol. 70, no. 18, pp. 4931-4947.
  • Ganguly, D, Stone, B, Bowerman, A et al. 2019, 'Excess Light Priming in Arabidopsis thaliana Genotypes with Altered DNA Methylomes', G3: Genes, Genomes, Genetics, vol. 9, no. 11, pp. 3611-3621.
  • Phua, S, Pornsiriwong, W, Chan, K et al 2018, 'Development of strategies for genetic manipulation and fine-tuning of a chloroplast retrograde signal 3 '-phosphoadenosine 5 '-phosphate', Plant Direct, vol. 2, no. 1, pp. 1-15.
  • Phua, S, Yan, D, Chan, K et al 2018, 'The arabidopsis SAL1-PAP pathway: A case study for integrating chloroplast retrograde, light and hormonal signaling in modulating plant growth and development?', Frontiers in Plant Science, vol. 9, no. 1171, pp. 1-8.
  • Crisp, P, Smith, A, Ganguly, D et al 2018, 'RNA polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling', Plant Physiology, vol. 178, no. 4, pp. 1614-1630pp.
  • Ganguly, DR, Crisp, P, Eichten, S Pogson, B 2018, Maintenance of pre-existing DNA methylation states through recurring excess-light stress, Plant Cell and Environment, vol. Accepted: 17 April 2018.
  • Zhang, X, Ivanova, A, Vandepoele, K et al 2017, 'The transcription factor MYB29 is a regulator of alternative oxidase1a', Plant Physiology, vol. 173, no. 3, pp. 1824-1843.
  • Cai, S, Chen, G, Wang, Y et al 2017, 'Evolutionary conservation of ABA signaling for stomatal closure', Plant Physiology, vol. 174, no. 2, pp. 732-747pp..
  • Pogson, B, Van Aken, O & Van Aken, O 2017, 'Convergence of mitochondrial and chloroplastic ANAC017/PAP-dependent retrograde signalling pathways and suppression of programmed cell death', Cell Death and Differentiation, vol. 24, no. 6, pp. 955-960.
  • Bose, J, Munns, R, Shabala, S et al 2017, 'Chloroplast function and ion regulation in plants growing on saline soils: Lessons from halophytes', Journal of Experimental Botany, vol. 68, no. 12, pp. 3129-3143.
  • Crisp, P, Ganguly, D, Smith, A et al 2017, 'Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis', The Plant Cell, vol. 29, no. 8, pp. 1836-1863.
  • Ganguly, D, Crisp, P, Eichten, S et al 2017, 'The Arabidopsis DNA methylome is stable under transgenerational drought stress', Plant Physiology, vol. 175, pp. 1893 - 1912.
  • Osmond, C, Chow, W, Wyber, R et al 2017, 'Relative functional and optical absorption cross-sections of PSII and other photosynthetic parameters monitored in situ,at a distance with a time resolution of a few seconds, using aprototype light induced fluorescence transient (LIFT) device', Functional Plant Biology, vol. 44, pp. 985-1006pp.
  • Ganguly, DR, Crisp, P, Eichten, S et al 2017, 'The Arabidopsis DNA methylome is stable under transgenerational drought stress', Plant Physiology, vol. 175, pp. 1893 - 1912.
  • Pornsiriwong, W, Estavillo, G, Chan, K ... Phua, S, et al 2017, 'A chloroplast retrograde signal, 3'-phosphoadenosine 5'-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination', eLife, vol. 6, no. -, pp. 1-34pp.
  • Chan, K, Mabbitt, P, Phua, S et al 2016, 'Sensing and signaling of oxidative stress in chloroplasts by inactivation of the SAL1 phosphoadenosine phosphatase', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 113, no. 31, pp. E4567-E4576.
  • Hou, X, Rivers, J, León, P et al 2016, 'Synthesis and Function of Apocarotenoid Signals in Plants', Trends in Plant Science, vol. 21, no. 9, pp. 792-803pp.
  • Crisp, P, Ganguly, D, Eichten, S et al 2016, 'Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics', Science Advances, vol. 2, no. 2, pp. e1501340-e1501340.
  • Chan, K, Phua, S, Crisp, P et al 2016, 'Learning the Languages of the Chloroplast: Retrograde Signaling and Beyond', Annual Review of Plant Biology, vol. 67, pp. 25-53.
  • Rungrat, T, Awlia, M, Brown, T et al 2016, 'Using Phenomic Analysis of Photosynthetic Function for Abiotic Stress Response Gene Discovery', The Arabidopsis Book, vol. 14, no. e0185, pp. 14pp..
  • Bowerman, A, Newberry, M, Dielen, A et al 2016, 'Suppression of glucan, water dikinase in the endosperm alters wheat grain properties, germination and coleoptile growth', Plant Biotechnology Journal, 14, p 398-408.
  • Bruggeman, Q, Mazubert, C, Prunier, F ... Phua, S, et al 2016, 'Chloroplast activity and 3' phosphadenosine 5'phosphate signaling regulate programmed cell death in Arabidopsis', Plant Physiology, vol. 170, no. 3, pp. 1745-1756.
  • Carmody, M, Crisp, P, d' Alessandro, S, Ganguly D, Gordon M, Havaux M, and Pogson BJ 2016, 'Uncoupling High Light Responses from Singlet Oxygen Retrograde Signaling and Spatial-Temporal Systemic Acquired Acclimation', Plant Physiology, vol. 171, no. 3, pp. 1734-1749.
  • Merchant, S, Bednarek, S, Birchler, J et al 2015, 'The Plant Cell Introduces Breakthrough Reports: A New Forum for Cutting-Edge Plant Research', The Plant Cell, vol. 27, no. 10, pp. 2667-2668pp.
  • Ganguly, D, Crisp, P, Harter, K et al 2015, 'Genetic suppression of plant development and chloroplast biogenesis via the Snowy Cotyledon 3 and Phytochrome B pathways', Functional Plant Biology, vol. 42, no. 7, pp. 676-686pp.
  • Pogson, B, Ganguly, D & Albrecht, V 2015, 'Insights into chloroplast biogenesis and development', Biochimica et Biophysica Acta: Bioenergetics, vol. 1847, no. 9, pp. 1017-1024.
  • Yin, C, Ma, B, Collinge, D et al 2015, 'Ethylene responses in rice roots and coleoptiles are differentially regulated by a carotenoid isomerase-mediated abscisic acid pathway', The Plant Cell, vol. 27, no. 4, pp. 1061-1081.
  • Rivers, J, Warthmann, N, Pogson, B et al 2015, 'Genomic breeding for food, environment and livelihoods', Food Security, vol. 7, no. 2, pp. 375-382.
  • Zhang, J, Yuan, H, Fei, Z et al 2015, 'Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp pekinensis)', Planta, vol. 241, no. 6, pp. 1381-1394pp.
  • McQuinn, R, Giovannoni, J & Pogson, B 2015, 'More than meets the eye: From carotenoid biosynthesis, to new insights into apocarotenoid signaling', Current Opinion in Plant Biology, vol. 27, pp. 172-179.
  • Nisar, N, Li, L, Lu, S et al 2015, 'Carotenoid Metabolism in Plants', Molecular Plant, vol. 8, no. 1, pp. 68-82.
  • Brown, T, Cheng, R, Sirault, X et al 2014, 'TraitCapture: genomic and environment modelling of plant phenomic data', Current Opinion in Plant Biology, vol. 18, pp. 73-79.
  • Estavillo, G, verhertbruggen, Y, Scheller, H et al 2014, 'Isolation of the plant cytosolic fraction for proteomic analysis', Methods in Molecular Biology, vol. 1072, pp. 453-467.
  • Brown, T, Cheng, R, Sirault, X et al 2014, 'TraitCapture: genomic and environment modelling of plant phenomic data', Current Opinion in Plant Biology, vol. 18, pp. 73-79.
  • Van Norman, J, Zhang, J, Cazzonelli, C et al 2014, 'Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative', National Academy of Sciences. Proceedings, vol. 111, no. 13, pp. E1300-E1309.
  • Cazzonelli, C, Nisar, N, Roberts, A et al 2014, 'A chromatin modifying enzyme, SDG8, is involved in morphological, gene expression, and epigenetic responses to mechanical stimulation', Frontiers in Plant Science, vol. 5, no. OCT, pp. 533-533.
  • Avendaño-Vázquez O, Cordoba E, Román CS, Nisar N, Cazzonelli C et al 2014, 'An uncharacterized apocarotenoid-derived signal generated in ?-carotene desaturase mutants regulates leaf development and the expression of chloroplast and nuclear genes in Arabidopsis', The Plant Cell, vol. 26, no. 6, pp. 2524-2537.
  • Pogson, B & Albrecht, V 2014, 'An Overview of Chloroplast Biogenesis and Development', in Steve M Theg & Francis-Andre Wollman (ed.), Plastid Biology, Springer, New York, pp. 115- 128.
  • Carmody, M & Pogson, B 2013, 'Systemic Photooxidative Stress Signalling', in Frantisek Baluska (ed.), Long-Distance Systemic Signaling and Communication in Plants, Springer, Berlin.
  • Chan, K, Wirtz, M, Phua, S et al 2013, 'Balancing metabolites in drought: the sulfur assimilation conundrum', Trends in Plant Science, vol. 18, no. 1, pp. 18-29.
  • Caliandro, R, Nagel, K, Kastenholz, B et al 2013, 'Effects of altered α- and β-branch carotenoid biosynthesis on photoprotection and whole-plant acclimation of Arabidopsis to photo-oxidative stress', Plant Cell and Environment, vol. 36, no. 2, pp. 438-453.
  • Jung, H, Crisp, P, Estavillo, G et al 2013, 'Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 35, pp. 14474-14479.
  • Albrecht, V, Kauss, D, Fan, D et al 2013, 'A novel proteinase, SNOWY COTYLEDON4, is required for photosynthetic acclimation to higher light intensities in Arabidopsis', Plant Physiology, vol. 163, no. 2, pp. 732-745.
  • Gordon, M, Carmody, M, Albrecht, V, and Pogson BJ 2013, 'Systemic and Local Responses to Repeated HL Stress-Induced Retrograde Signaling in Arabidopsis', Frontiers in Plant Science, vol. 3, no. Article 303, pp. 1-20.
  • Jia, H, Forster, B, Chow, W et al 2013, 'Decreased Photochemical Efficiency of Photosystem II following Sunlight Exposure of Shade-Grown Leaves of Avocado: Because of, or in Spite of, Two Kinetically Distinct Xanthophyll Cycles?', Plant Physiology, vol. 161, no. 2, pp. 836-852.
  • Matsubara, S, Foerster, B, Waterman, M et al 2012, 'From ecophysiology to phenomics: some implications of photoprotection and shade-sun acclimation in situ for dynamics of thylakoids in vitro', Philosophical Transactions of the Royal Society of London Series B, vol. 367, no. 1608, pp. 3503-3514.
  • Zhang, B, Zhang, B, Carrie, C et al 2012, 'LETM proteins play a role in the accumulation of mitochondrially encoded proteins in Arabidopsis thaliana and AtLETM2 displays parent of origin effects', Journal of Biological Chemistry, vol. 287, no. 50, pp. 41757-41773.
  • Tanz, S, Killian, J, Johnsson, C et al 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', The Plant Journal, vol. 69, no. 5, pp. 743-754.
  • Nisar, N, Verma, S, Pogson, B et al 2012, 'Inflorescence stem grafting made easy in Arabidopsis', Plant Methods, vol. 8, no. 50, pp. -.
  • Estavillo, G, Crisp, P, Pornsiriwong, W et al 2011, 'Evidence for a SAL1-PAP Chloroplast Retrograde Pathway That Functions in Drought and High Light Signaling in Arabidopsis', The Plant Cell, vol. 23, no. 11, pp. 3992-4012.
  • Pogson, B & Albrecht, V 2011, 'Genetic Dissection of Chloroplast Biogenesis and Development: An Overview', Plant Physiology, vol. 155, no. 4, pp. 1545-1551.
  • Forster, B & Osmond, CB, Pogson BJ 2011, 'Lutein from deepoxidation of lutein epoxide replaces zeaxanthin to sustain an enhanced capacity for nonphotochemical chlorophyll fluorescence quenching in avocado shade leaves in the dark', Plant Physiology, 156, no. 1, pp. 393-403.
  • Cazzonelli, C & Pogson, B 2010, 'Source to sink: regulation of carotenoid biosynthesis in plants', Trends in Plant Science, vol. 15, no. 5, pp. 266-274.
  • Meyer, E, Tomaz, T, Carroll, A et al 2009, 'Remodeled respiration in ndufs4 with low phosphorylation efficiency suppresses Arabidopsis germination and growth and alters control of metabolism at night', Plant Physiology, vol. 151, no. 2, pp. 603-619.
  • Howitt, C, Cavanagh, C, Bowerman, A et al 2009, 'Alternative splicing, activation of cryptic exons and amino acid substitutions in carotenoid biosynthetic genes are associated with lutein accumulation in wheat endosperm', Functional & Integrative Genomics, vol. 9, pp. 363-376.
  • Giraud, E, Ho, L, Clifton, R et al 2008, 'The Absence of ALTERNATIVE OXIDASE1a in Arabidopsis Results in Acute Sensitivity to Combined Light and Drought Stress', Plant Physiology, vol. 147, pp. 595-610.
  • Albrecht, V, Simkova, K, Carrie, C et al 2010, 'The Cytoskeleton and the Peroxisomal-Targeted SNOWY COTYLEDON3 Protein Are Required for Chloroplast Development in Arabidopsis', The Plant Cell, vol. 22, no. 10, pp. 3423-3438.
  • Cazzonelli, C, Roberts, A, Carmody, M, and Pogson BJ 2010, 'Transcriptional Control of SET DOMAIN GROUP 8 and CAROTENOID ISOMERASE during Arabidopsis Development', Molecular Plant, vol. 3, no. 1, pp. 174-191.
  • Meyer, E, Tomaz, T, Carroll, A et al 2009, 'Remodeled respiration in ndufs4 with low phosphorylation efficiency suppresses Arabidopsis germination and growth and alters control of metabolism at night', Plant Physiology, vol. 151, no. 2, pp. 603-619.
  • Bond, D, Dennis, E, Pogson, B et al 2009, 'Histone Acetylation, VERNALIZATION INSENSITIVE 3, FLOWERING LOCUS C, and the Vernalization Response', Molecular Plant, vol. 2, no. 4, pp. 724-737.
  • Howitt, C, Cavanagh, C, Bowerman, A et al 2009, 'Alternative splicing, activation of cryptic exons and amino acid substitutions in carotenoid biosynthetic genes are associated with lutein accumulation in wheat endosperm', Functional & Integrative Genomics, vol. 9, pp. 363-376.
  • Wilson, P, Estavillo, G, Field, K et al 2009, 'The nucleotidase/phosphatase SAL1 is a negative regulator of drought tolerance in Arabidopsis', The Plant Journal, vol. 58, no. 2, pp. 299-317.
  • Miller, A, Carrie, C, Pogson, B et al 2009, 'Exploring the function:location Nexus - using multiple lines of evidence in defining the subcellular location of plant proteins', The Plant Cell, vol. 21, no. 6, pp. 1625-1631.
  • Cazzonelli, C, Cuttriss, A, Cossetto, S et al 2009, 'Regulation of Carotenoid Composition and Shoot Branching in Arabidopsis by a Chromatin Modifying Histone Methyltransferase, SDG8', The Plant Cell, vol. 21, no. 1, pp. 39-53.
  • Wilson, P, Estavillo, G, Field, K et al 2009, 'The nucleotidase/phosphatase SAL1 is a negative regulator of drought tolerance in Arabidopsis', The Plant Journal, vol. 58, no. 2, pp. 299-317.
  • Forster, B, Pogson, BJ, Osmond CB 2009, 'De Novo Synthesis and Degradation of Lx and V Cycle Pigments during Shade and Sun Acclimation in Avocado Leaves', Plant Physiology, vol. 149, pp. 1179-1195.
  • Pogson, B, Woo, N, Foerster, B et al 2008, 'Plastid signalling to the nucleus and beyond', Trends in Plant Science, vol. 13, no. 11, pp. 602-609.
  • Rossel, J, Wilson, P, Hussain, D et al 2007, 'Systemic and Intracellular responses to PhotoOxidative Sress in Arabidopsis', The Plant Cell, vol. 19, pp. 4091-4110.
  • DellaPenna, D & Pogson, B 2006, 'Vitamin Synthesis in Plants: Tocopherols and Carotenoids', Annual Review of Plant Biology, vol. 57, pp. 711-738.
  • Millgate, A, Pogson, B, Wilson, I et al 2004, 'Morphine-pathway block in top1 poppies', Nature, vol. 431, no. 7007, pp. 413-414.
  • Park, H, Kreunen, S, Cuttriss, A et al 2002, 'Identification of the Carotenoid Isomerase Provides Insight into Carotenoid Biosynthesis, Prolamellar Body Formation, and Photomorphogenesis', The Plant Cell, vol. 14, pp. 321-332.