Barry J Pogson

Australian National University, Canberra, Australian Capital Territory, Australia

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Publications (93)542.81 Total impact

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    ABSTRACT: Programmed cell death (PCD) is a crucial process both for plant development and responses to biotic and abiotic stress. There is accumulating evidence that chloroplasts may play a central role during plant PCD as for mitochondria in animal cells, but it is still unclear whether they participate in PCD onset, execution or both. To tackle this question, we have analyzed the contribution of chloroplast function to the cell death phenotype of the mips1 mutant that forms spontaneous lesions in a light-dependent manner. We show that photosynthetically-active chloroplasts are required for PCD to occur in mips1, but this process is independent of the redox state of the chloroplast. Systematic genetic analyses with retrograde signaling mutants reveal that 3'-phosphoadenosine 5'-phosphate (PAP), a chloroplast retrograde signal that modulates nuclear gene expression in response to stress, can inhibit cell death and compromises plant innate immunity via inhibition of the RNA-processing 5'-3' exoribonucleases (XRNs). Our results provide evidence for the role of chloroplast-derived signal and RNA metabolism in the control of cell death and biotic stress response.
    No preview · Article · Jan 2016 · Plant physiology
  • Kai Xun Chan · Su Yin Phua · Peter Crisp · Ryan McQuinn · Barry J Pogson
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    ABSTRACT: The chloroplast can act as an environmental sensor, communicating with the cell during biogenesis and operation to change the expression of thousands of proteins. This process, termed retrograde signaling, regulates expression in response to developmental cues and stresses that affect photosynthesis and yield. Recent advances have identified many signals and pathways-including carotenoid derivatives, isoprenes, phosphoadenosines, tetrapyrroles, and heme, together with reactive oxygen species and proteins-that build a communication network to regulate gene expression, RNA turnover, and splicing. However, retrograde signaling pathways have been viewed largely as a means of bilateral communication between organelles and nuclei, ignoring their potential to interact with hormone signaling and the cell as a whole to regulate plant form and function. Here, we discuss new findings on the processes by which organelle communication is initiated, transmitted, and perceived, not only to regulate chloroplastic processes but also to intersect with cellular signaling and alter physiological responses. Expected final online publication date for the Annual Review of Plant Biology Volume 67 is April 29, 2016. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
    No preview · Article · Jan 2016 · Annual Review of Plant Biology
  • Ryan P McQuinn · James J Giovannoni · Barry J Pogson
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    ABSTRACT: Carotenoids are a class of isoprenoids synthesized almost exclusively in plants involved in a myriad of roles including the provision of flower and fruit pigmentation for the attraction of pollinators and seed dispersing organisms. While carotenoids are essential throughout plant development, they are also extremely important in human diets providing necessary nutrition and aiding in the prevention of various cancers, age-related diseases and macular degeneration. Utilization of multiple plant models systems (i.e. Arabidopsis; maize; and tomato) has provided a comprehensive framework detailing the regulation of carotenogenesis throughout plant development covering all levels of genetic regulation from epigenetic to post-translational modifications. That said, the understanding of how carotenoids self-regulate remains fragmented. Recent reports demonstrate the potential influence of carotenoid-cleavage products (apocarotenoids) as signaling molecules regulating carotenoid biosynthesis in addition to various aspects of plants development (i.e. leaf and root development). This review highlights recent advances in carotenogenic regulation and insights into potential roles of novel apocarotenoids in plants. Copyright © 2015 Elsevier Ltd. All rights reserved.
    No preview · Article · Aug 2015 · Current opinion in plant biology
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    ABSTRACT: Starch phosphate ester content is known to alter the physicochemical properties of starch, including its susceptibility to degradation. Previous work producing wheat (Triticum aestivum) with down-regulated glucan, water dikinase, the primary gene responsible for addition of phosphate groups to starch, in a grain-specific manner found unexpected phenotypic alteration in grain and growth. Here, we report on further characterization of these lines focussing on mature grain and early growth. We find that coleoptile length has been increased in these transgenic lines independently of grain size increases. No changes in starch degradation rates during germination could be identified, or any major alteration in soluble sugar levels that may explain the coleoptile growth modification. We identify some alteration in hormones in the tissues in question. Mature grain size is examined, as is Hardness Index and starch conformation. We find no evidence that the increased growth of coleoptiles in these lines is connected to starch conformation or degradation or soluble sugar content and suggest these findings provide a novel means of increasing coleoptile growth and early seedling establishment in cereal crop species. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
    Full-text · Article · May 2015 · Plant Biotechnology Journal
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    ABSTRACT: Ethylene and abscisic acid (ABA) act synergistically or antagonistically to regulate plant growth and development. ABA is derived from the carotenoid biosynthesis pathway. Here, we analyzed the interplay among ethylene, carotenoid biogenesis, and ABA in rice (Oryza sativa) using the rice ethylene response mutant mhz5, which displays a reduced ethylene response in roots but an enhanced ethylene response in coleoptiles. We found that MHZ5 encodes a carotenoid isomerase and that the mutation in mhz5 blocks carotenoid biosynthesis, reduces ABAaccumulation, and promotes ethylene production in etiolated seedlings. ABA can largely rescue the ethylene response of the mhz5 mutant. Ethylene induces MHZ5expression, the production of neoxanthin, an ABA biosynthesis precursor, andABA accumulation in roots. MHZ5 overexpression results in enhanced ethylene sensitivity in roots and reduced ethylene sensitivity in coleoptiles. Mutation or overexpression of MHZ5 also alters the expression of ethylene-responsive genes. Genetic studies revealed that the MHZ5-mediated ABA pathway acts downstream of ethylene signaling to inhibit root growth. The MHZ5-mediated ABA pathway likely acts upstream but negatively regulates ethylene signaling to control coleoptile growth. Our study reveals novel interactions among ethylene, carotenogenesis, and ABA and provides insight into improvements in agronomic traits and adaptive growth through the manipulation of these pathways in rice.
    Full-text · Article · Apr 2015 · The Plant Cell
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    Junxiang Zhang · Hui Yuan · Zhangjun Fei · Barry J Pogson · Lugang Zhang · Li Li
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    ABSTRACT: Main conclusion: The orange head phenotype of Br - or resulted from a large insertion in carotenoid isomerase (BrCRTISO) . Comparative transcriptome analysis revealed that the mutation affected the expression of abundant transcription factor genes. A new orange trait-specific marker was developed for marker-assisted breeding. Orange head leaves are a desirable quality trait for Chinese cabbage. Our previous fine mapping identified BrCRTISO as the Br-or candidate gene for the orange Chinese cabbage mutant. Here, we examined the BrCRTISO gene from white and orange head Chinese cabbage. While BrCRTISO from the white control plant was able to complement the Arabidopsis Atcrtiso mutant phenotype, Brcrtiso with a large insertion from the orange head Chinese cabbage failed to rescue the Arabidopsis mutant phenotype. The results show that Brcrtiso was non-functional, concomitant with the accumulation of prolycopene in Br-or to yield orange head. Comparative transcriptome analysis by RNA-seq identified 372 differentially expressed genes between the control and Br-or mutant using two near-isogenic lines with white and orange inner leaves. The mutation in BrCRTISO specifically affected many genes in the functional groups involved in RNA, protein, transport, and signaling. Particularly, expressions of many transcription factor genes were dramatically altered in Br-or, suggesting a potential role of BrCRTISO or carotenoid metabolites in affecting transcription. A novel co-dominant gene-specific marker was developed that co-segregated with orange color phenotype and would be useful for marker-assisted selection with enhanced selection efficiency. Our study provides new insights into understanding of the molecular basis of Br-or in mediating head leaf color and depicts a global view of the effect of BrCRTISO on cellular processes in plant. It also provides a molecular tool to accelerate breeding new Chinese cabbage cultivars with unique health quality and visual appearance.
    Full-text · Article · Feb 2015 · Planta
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    Barry J Pogson · Diep Ganguly · Verónica Albrecht-Borth
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    ABSTRACT: In recent years many advances have been made to obtain insight into chloroplast biogenesis and development. In plants several plastids types exist such as the proplastid (which is the progenitor of all plastids), leucoplasts (group of colourless plastids important for storage including elaioplasts (lipids), amyloplasts (starch) or proteinoplasts (proteins)), chromoplasts (yellow to orange-coloured due to carotenoids, in flowers or in old leaves as gerontoplasts), and the green chloroplasts. Chloroplasts are indispensable for plant development; not only by performing photosynthesis and thus rendering the plant photoautotrophic, but also for biochemical processes (which in some instances can also take place in other plastids types), such as the synthesis of pigments, lipids, and plant hormones and sensing environmental stimuli. Although we understand many aspects of these processes there are gaps in our understanding of the establishment of functional chloroplasts and their regulation. Why is that so? Even though chloroplast function is comparable in all plants and most of the algae, ferns and moss, detailed analyses have revealed many differences, specifically with respect to its biogenesis. As an update to our prior review on the genetic analysis of chloroplast biogenesis and development [1] herein we will focus on recent advances in Angiosperms (monocotyledonous and dicotyledonous plants) that provide novel insights and highlight the challenges and prospects for unravelling the regulation of chloroplast biogenesis specifically during the establishment of the young plants. This article is part of a Special Issue entitled: Chloroplast Biogenesis. Copyright © 2015. Published by Elsevier B.V.
    Full-text · Article · Feb 2015 · Biochimica et Biophysica Acta (BBA) - Bioenergetics
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    Nazia Nisar · Li Li · Shan Lu · Nay Chi Khin · Barry J Pogson
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    ABSTRACT: Carotenoids are mostly C40 terpenoids, a class of hydrocarbons that participate in various biological processes in plants, such as photosynthesis, photomorphogenesis, photoprotection, and development. Carotenoids also serve as precursors for two plant hormones and a diverse set of apocarotenoids. They are colorants and critical components of the human diet as antioxidants and provitamin A. In this review, we summarize current knowledge of the genes and enzymes involved in carotenoid metabolism and describe recent progress in understanding the regulatory mechanisms underlying carotenoid accumulation. The importance of the specific location of carotenoid enzyme metabolons and plastid types as well as of carotenoid-derived signals is discussed. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.
    Full-text · Article · Jan 2015 · Molecular Plant
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    ABSTRACT: Plant development is regulated by external and internal factors such as light and chloroplast development. A revertant of the Arabidopsis thaliana (L.) Heyhn. chloroplast biogenesis mutant snowy cotyledon 3 (sco3-1) was isolated partially recovering the impaired chloroplast phenotype. The mutation was identified in the Phytochrome B (PhyB) gene and is a result of an amino acid change within the PAS repeat domain required for light-induced nuclear localisation. An independent phyB-9 mutation was crossed into sco3-1 mutants, resulting in the same partial reversion of sco3-1. Further analysis demonstrated that SCO3 and PhyB influence the greening process of seedlings and rosette leaves, embryogenesis, rosette formation and flowering. Interestingly, the functions of these proteins are interwoven in various ways, suggesting a complex genetic interaction. Whole-transcriptome profiling of sco3-1phyB-9 indicated that a completely distinct set of genes was differentially regulated in the double mutant compared with the single sco3-1 or phyB-9 mutants. Thus, we hypothesise that PhyB and SCO3 genetically suppress each other in plant and chloroplast development.
    Full-text · Article · Jan 2015 · Functional Plant Biology
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    ABSTRACT: Thigmomorphogenesis is viewed as being a response process of acclimation to short repetitive bursts of mechanical stimulation or touch. The underlying molecular mechanisms that coordinate changes in how touch signals lead to long-term morphological changes are enigmatic. Touch responsive gene expression is rapid and transient, and no transcription factor or DNA regulatory motif has been reported that could confer a genome wide mechanical stimulus. We report here on a chromatin modifying enzyme, SDG8/ASHH2, which can regulate the expression of many touch responsive genes identified in Arabidopsis. SDG8 is required for the permissive expression of touch induced genes; and the loss of function of sdg8 perturbs the maximum levels of induction on selected touch gene targets. SDG8 is required to maintain permissive H3K4 trimethylation marks surrounding the Arabidopsis touch-inducible gene TOUCH 3 (TCH3), which encodes a calmodulin-like protein (CML12). The gene neighboring was also slightly down regulated, revealing a new target for SDG8 mediated chromatin modification. Finally, sdg8 mutants show perturbed morphological response to wind-agitated mechanical stimuli, implicating an epigenetic memory-forming process in the acclimation response of thigmomorphogenesis.
    Full-text · Article · Oct 2014 · Frontiers in Plant Science
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    ABSTRACT: In addition to acting as photoprotective compounds, carotenoids also serve as precursors in the biosynthesis of several phytohormones and proposed regulatory signals. Here, we report a signaling process derived from carotenoids that regulates early chloroplast and leaf development. Biosynthesis of the signal depends on ζ-carotene desaturase activity encoded by the ζ-CAROTENE DESATURASE (ZDS)/CHLOROPLAST BIOGENESIS5 (CLB5) gene in Arabidopsis thaliana. Unlike other carotenoid-deficient plants, zds/clb5 mutant alleles display profound alterations in leaf morphology and cellular differentiation as well as altered expression of many plastid- and nucleus-encoded genes. The leaf developmental phenotypes and gene expression alterations of zds/clb5/spc1/pde181 plants are rescued by inhibitors or mutations of phytoene desaturase, demonstrating that phytofluene and/or ζ-carotene are substrates for an unidentified signaling molecule. Our work further demonstrates that this signal is an apocarotenoid whose synthesis requires the activity of the carotenoid cleavage dioxygenase CCD4.
    Full-text · Article · Jun 2014 · The Plant Cell
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    ABSTRACT: In plants, continuous formation of lateral roots (LRs) facilitates efficient exploration of the soil environment. Roots can maximize developmental capacity in variable environmental conditions through establishment of sites competent to form LRs. This LR prepattern is established by a periodic oscillation in gene expression near the root tip. The spatial distribution of competent (prebranch) sites results from the interplay between this periodic process and primary root growth; yet, much about this oscillatory process and the formation of prebranch sites remains unknown. We find that disruption of carotenoid biosynthesis results in seedlings with very few LRs. Carotenoids are further required for the output of the LR clock because inhibition of carotenoid synthesis also results in fewer sites competent to form LRs. Genetic analyses and a carotenoid cleavage inhibitor indicate that an apocarotenoid, distinct from abscisic acid or strigolactone, is specifically required for LR formation. Expression of a key carotenoid biosynthesis gene occurs in a spatially specific pattern along the root's axis, suggesting spatial regulation of carotenoid synthesis. These results indicate that developmental prepatterning of LRs requires an uncharacterized carotenoid-derived molecule. We propose that this molecule functions non-cell-autonomously in establishment of the LR prepattern.
    No preview · Article · Mar 2014 · Proceedings of the National Academy of Sciences
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    ABSTRACT: Agriculture requires a second green revolution to provide increased food, fodder, fiber, fuel and soil fertility for a growing population while being more resilient to extreme weather on finite land, water, and nutrient resources. Advances in phenomics, genomics and environmental control/sensing can now be used to directly select yield and resilience traits from large collections of germplasm if software can integrate among the technologies. Traits could be Captured throughout development and across environments from multi-dimensional phenotypes, by applying Genome Wide Association Studies (GWAS) to identify causal genes and background variation and functional structural plant models (FSPMs) to predict plant growth and reproduction in target environments. TraitCapture should be applicable to both controlled and field environments and would allow breeders to simulate regional variety trials to pre-select for increased productivity under challenging environments.
    Full-text · Article · Mar 2014 · Current Opinion in Plant Biology
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    ABSTRACT: Cellular auxin homeostasis controls many aspects of plant growth, organogenesis and development. The existence of intracellular auxin transport mediated by endoplasmic reticulum (ER)-localized PIN5, PIN6 and PIN8 proteins is a relatively recent discovery shaping a new era in understanding auxin-mediated growth processes. Here we summarize the importance of PIN6 in mediating intracellular auxin transport during root formation, leaf vein patterning and nectary production. While, it was previously shown that PIN6 was strongly expressed in rosette leaf cell types important in vein formation, here we demonstrate by use a PIN6 promoter-reporter fusion, that PIN6 is also preferentially expressed in the vasculature of the primary root, cotyledons, cauline leaves, floral stem, sepals and the main transmitting tract of the reproductive silique. The strong, vein- specific reporter gene expression patterns enabled by the PIN6 promoter emphasizes that transcriptional control is likely to be a major regulator of PIN6 protein levels, during vasculature formation, and supports the need for ER-localized PIN proteins in selecting specialized cells for vascular function in land plants.
    No preview · Article · Jan 2014 · Plant signaling & behavior
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    ABSTRACT: The cytosol is the fluid portion of the cell that is not partitioned by membranes. It contains a highly diverse collection of substances and is central to many essential cellular processes ranging from signal transduction, metabolite production and transport, protein biosynthesis and degradation to stress response and defense. Despite its importance, only a few proteomic studies have been performed on the plant cytosol. This is largely due to difficulties in isolating relatively pure samples from plant material free of disrupted organelle material. In this chapter we outline methods for isolating the cytosolic fraction from Arabidopsis cell cultures and seedlings and provide guidance on assessing purity for analysis by mass spectrometry.
    No preview · Article · Jan 2014 · Methods in molecular biology (Clifton, N.J.)
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    ABSTRACT: Excess light can have a negative impact on photosynthesis, thus plants have evolved many different ways to adapt to different light conditions to both optimize energy use and avoid damage caused by excess light. Analysis of the snowy cotyledon 4 (sco4) mutant revealed a mutation in a chloroplast-targeted protein which shares limited homology with CaaX-type-endopeptidases. The SCO4 protein possesses an important function in photosynthesis and development, with point mutations rendering the seedlings and adult plants susceptible to photo-oxidative stress. The sco4 mutation impairs acclimation of chloroplasts and their photosystems to excess light, evidenced in a reduction in PS I function, decreased linear electron transfer, yet increased non-photochemical quenching. SCO4 is localized to the chloroplasts and suggests the existence of an unreported type of protein modification within this organelle. Phylogenetic and yeast complementation analyses of SCO4-like proteins reveals that SCO4 is a member of a unknown group of higher plant-specific proteinases quite distinct from the well described CaaX-type endopeptidases RCE1 and STE24 and lacks canonical CaaX activity. Therefore, we hypothesize that SCO4 is a novel endopeptidase required for critical protein modifications within chloroplasts, influencing the function of proteins involved in photosynthesis required for tolerance to excess light.
    Full-text · Article · Aug 2013 · Plant physiology
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    ABSTRACT: Background / Purpose: Plants have a range of photo-protective mechanisms to prevent damage. Looking for variations in natural populations may identify novel genes and alleles responsible for photoprotection. Main conclusion: Our preliminary results show that high throughput fluorescence imaging methods using TrayScan can be used to study photoprotective mechanisms in large populations. Using this method and analysis pipeline for QTL mapping we can identify novel genes which relate to non-photochemical quenching (NPQ).
    Preview · Conference Paper · Aug 2013
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    ABSTRACT: Sunlight provides energy for photosynthesis and is essential for nearly all life on earth. However, too much or too little light or rapidly fluctuating light conditions cause stress to plants. Rapid changes in the amount of light are perceived as a change in the reduced/oxidized (redox) state of photosynthetic electron transport components in chloroplasts. However, how this generates a signal that is relayed to changes in nuclear gene expression is not well understood. We modified redox state in the reference plant, Arabidopsis thaliana, using either excess light or low light plus the herbicide DBMIB (2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone), a well-known inhibitor of photosynthetic electron transport. Modification of redox state caused a change in expression of a common set of about 750 genes, many of which are known stress-responsive genes. Among the most highly enriched promoter elements in the induced gene set were heat-shock elements (HSEs), known motifs that change gene expression in response to high temperature in many systems. We show that HSEs from the promoter of the ASCORBATE PEROXIDASE 2 (APX2) gene were necessary and sufficient for APX2 expression in conditions of excess light, or under low light plus the herbicide. We tested APX2 expression phenotypes in overexpression and loss-of-function mutants of 15 Arabidopsis A-type heat-shock transcription factors (HSFs), and identified HSFA1D, HSFA2, and HSFA3 as key factors regulating APX2 expression in diverse stress conditions. Excess light regulates both the subcellular location of HSFA1D and its biochemical properties, making it a key early component of the excess light stress network of plants.
    Full-text · Article · Aug 2013 · Proceedings of the National Academy of Sciences
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    ABSTRACT: Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development.
    Full-text · Article · Jul 2013 · PLoS ONE
  • Melanie E. Carmody · Barry J. Pogson

    No preview · Chapter · Jan 2013

Publication Stats

5k Citations
542.81 Total Impact Points

Institutions

  • 2002-2015
    • Australian National University
      • • College of Medicine, Biology & Environment
      • • Division of Plant Sciences
      Canberra, Australian Capital Territory, Australia
  • 2008
    • University of Western Australia
      • ARC Centre of Excellence in Plant Energy Biology
      Perth City, Western Australia, Australia
  • 2007
    • Humboldt-Universität zu Berlin
      Berlín, Berlin, Germany
  • 2001-2004
    • Australian Society for Biochemistry and Molecular Biology
      Canberra, Australian Capital Territory, Australia
  • 1998-2001
    • Arizona State University
      Tempe, Arizona, United States
  • 1996
    • University of Nevada, Reno
      Reno, Nevada, United States
    • University of Liverpool
      • Department of Chemistry
      Liverpool, England, United Kingdom