Arabidopsis Research Roundup: October 21st

This weeks Roundup demonstrates a wide breadth of research topics that use Arabidopsis as the model organism. Firstly Matthew Terry and colleagues investigate the factors that control reterograde signaling between chloroplast and nucleus. Secondly researchers from the University of Sheffield demonstrate that a component of the cell wall is involved in stomatal opening. Thirdly Malcolm Bennett and Ranjan Swarup from CPIB are co-authors on research that touches on a familiar topic, the regulation of the AUX1 protein in Arabidopsis roots. Fourthly Alastair Rutherford is a collaborator on a US-led study that investigates the proton motion force across thylakoid membranes. Finally are two studies wherein UK academics, namely David Salt and Malcolm Hawkesford, are co-authors on German-led studies that investigate a plants response to different minerals.

Page MT, McCormac AC, Smith AG, Terry MJ (2016) Singlet oxygen initiates a plastid signal controlling photosynthetic gene expression. New Phytol.

Open Access
Matthew Terry (Southampton) is the lead author on this study that investigates the factors regulating retrograde signaling between chloroplast and nucleus. One model for the control of this process is based around a signal, which is abolished by the herbicide norflurazon, which is related to levels of haem in chloroplasts. In addition this reterograde signalling can be damaged by the transfer of seedlings from far-red to white light. This study investigates whether these external factors influence the same endogenous signal transduction pathway and show, perhaps surprisingly, that different sets of genes are mostly affected in each case. FR pretreatment results in the damaging production of singlet oxygen molecules, which is inhibited by a mutant that lacks a correct signaling pathway that responds to oxygen. The authors suggest that this control process, wherein the production of oxygen in the chloroplast is a signal for reduced photosynthetic gene expression, acts to fine tune this system in response to differing light conditions.


Amsbury S, Hunt L, Elhaddad N, Baillie A, Lundgren M, Verhertbruggen Y, Scheller HV, Knox JP, Fleming AJ, Gray JE (2016) Stomatal Function Requires Pectin De-methyl-esterification of the Guard Cell Wall. Current Biology

Open Access
This manuscript is led by Julie Gray and Andrew Fleming at the University of Sheffield and looks at how the composition of the plant cell wall can affect stomatal opening. They show that guard cell walls are rich in un-esterified pectins and that a pectin methylesterase gene, PME6, is required for stomatal function and appropriately is highly expressed in this tissue. Mutant pme6 plants have an altered cell wall composition alongside a reduction in the dynamics of stomatal opening, indicating that there is a mechanical constraint on the ability of their guard cell walls to move in an appropriate manner. Overall, pme6 plants show decreased growth, due to increased CO2 loss, a phenotype that can be rescued by growth in elevated CO2. Although it is well known that multiple signals converge to control stomatal movement, this manuscript introduces a downstream component to this pathway that links in the physical movement of the guard cell walls.


Street IH, Mathews DE, Yamburkenko MV, Sorooshzadeh A, John RT, Swarup R, Bennett MJ, Kieber JJ, Schaller GE (2016) Cytokinin acts through the auxin influx carrier AUX1 to regulate cell elongation in the root. Development

This paper features Malcolm Bennett and Ranjan Swarup from CPIB as co-authors on a paper led by US colleagues. The requirement for hormone crosstalk has long been known to be critical for the precise control of root development. This study shows the role of cytokinin in modulation of auxin activity in the lateral root cap is dependent on the auxin influx carrier AUX1. This is true of ethylene dependent and independent modes of cytokinin action. Furthermore an autoregulatory signalling loop is discovered that integrates the effects of cytokinin and auxin and features AUX1 as well as the auxin responsive transcription factor ARR10. This study adds further detail to our knowledge of the mechanisms by which cytokinin controls root growth via auxin transport.


Davis GA,, Kanazawa A,, Schöttler MA, Kohzuma K, Froehlich JE, Rutherford AW, Satoh-Cruz M, Minhas D, Tietz S, Dhingra A, Kramer DM (2016) Limitations to photosynthesis by proton motive force-induced photosystem II photodamage. Elife

Open Access

Alastair Rutherford (Imperial College) is a co-author on this study that is led by researchers at Michigan State. They use a range of Arabidopsis mutants that show altered thylakoid lumen proton efflux to investigate their effect on the thylakoid proton motive force (pmf). PMF is required for the production of ATP and concomitantly could be considered essential for life on Earth. These mutants show alterations in photosynthetic regulation as well as on levels of photosystem II photodamage. More detailed measurements show that these phenotypes are dependent on an elevated electric field across the thylakoid, which alters the activity of PSII and its subsequent photodamage through production of destructive oxygen species. This alteration in the electric field across the thylakoid is important in wildtype plants and the authors suggest that the photodamage that naturally occurs in fluctuating light conditions could represent a limiting factor for plant productivity.


Kühnlenz T, Hofmann C, Uraguchi S, Schmidt H, Schempp S, Weber M, Lahner B, Salt DE, Clemens S (2016) Phytochelatin Synthesis Promotes Leaf Zn Accumulation of Arabidopsis thaliana Plants Grown in Soil with Adequate Zn Supply and is Essential for Survival on Zn-contaminated Soil. Plant Cell Physiol.

Open Access
Current GARNet Chairman and a recent arrival at CPIB in Nottingham, David Salt is a co-author on this German-led paper that assesses the role of Phytochelatin (PC) on plant growth in zinc contaiminated soils. PC is known to be essential for metal detoxification yet its role in zinc tolerance is not fully appreciated. Therefore wildtype and PC mutant (atpcs1) Arabidopsis were grown in soil with varying zinc concentrations. High concentrations of zinc cause PC upregulation, a response that is significantly compromised in atpcs1 mutant plants. Interestingly mutant plants show differing zinc levels when compared to wildtype in either normal or zinc-limited conditions. Finally the authors dissect the regulatory elements within AtPCS1 protein, showing that there are distinct domains that are responsible for activation by zinc or cadmium. This is indicative of a level of differential activity and is suggestive of the presence of multiple signaling pathways to deal with metal accumulation.

Forieri I, Sticht C, Reichelt M, Gretz N, Hawkesford MJ, Malagoli M, Wirtz M, Hell R (2016) Systems analysis of metabolism and the transcriptome in Arabidopsis thaliana roots reveals differential co-regulation upon iron, sulfur and potassium deficiency. Plant Cell Environ.

Open Access

This German-led study includes Malcolm Hawkesford (Rothamstead Research) and investigates shoot growth under iron, potassium or sulfur deficiency. When these minerals were adjusted to cause equivalent alterations in shoot growth they showed specific morphological alterations, changes in root metabolic profiles and in transcriptional responses. Iron deficiency causes the strongest gene expression changes, altering up to 18% of the transcriptome. A surprisingly small number of genes (180) were co-regulated by all of the nutrients. Iron deficiency alters a different set of genes involved in sulfur regulation compared to those observed in conditions of sulfur deficiency itself, indicative of mineral-specific cross-regulation of response pathways. Overall these experiments enable the dissection of general stress responses from those induced by specific deficiencies at the metabolic and transcriptomic scales.

Arabidopsis Research Roundup: October 6th.

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Published on: October 6, 2016

This week Arabidopsis Research Roundup includes an audio description from Robert Sablowski about work from this lab that describes the early specification of stem tissue within the shoot apical meristem. In addition multiple members of CPIB in Nottingham are involved in two connected papers that describe how auxin homeostasis is controlled at the cell and tissue level. Researchers from the University of Bristol shed light on the relationship between viral infection and stomatal development whilst Claudius Marondedze from the University of Cambridge in involved in a study that has used next generation lighting technology to grow Arabidopsis. Finally Sean May from NASC is a co-author on a study that looks into the role of brassinosteroid on the response to freezing temperatures.

Bencivenga S, Serrano-Mislata A, Bush M, Fox S, Sablowski R (2016) Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis. Dev Cell. S1534-5807(16)30588-3 Open Access

Robert Sablowski (John Innes Centre) is the lead author on this study that investigates the origin of Arabidopsis stem tissue within the shoot apical meristem (SAM). They show that the transcription factor REPLUMLESS (RPL) is responsible for patterning in the central and peripheral regions of the Rib Zone, which is a subset of cells within the SAM. The authors identify genes that are targeted by RPL, including LIGHT-SENSITIVE HYPOCOTYL 4 that had been previously identified as an organ boundary gene and in this context is involved in the same signaling pathway as RPL. This work opens up new avenues to research stem development, which is a critical yet little studied aspect of plant growth.

Professor Sablowski kindly provides an audio description of this work.

On an additional note, last year Robert collaborated with Maddie Moate to produce an excellent video about meristems!

Porco S, Pěnčík A, Rashed A, Voß U, Casanova-Sáez R, Bishopp A, Golebiowska A, Bhosale R, Swarup R, Swarup K, Peňáková P, Novák O, Staswick P, Hedden P, Phillips AL, Vissenberg K, Bennett MJ, Ljung K (2016) Dioxygenase-encoding AtDAO1 gene controls IAA oxidation and homeostasis in Arabidopsis. PNAS Open Access

Mellor N, Band LR, Pěnčík A, Novák O, Rashed A, Holman T, Wilson MH, Voß U, Bishopp A, King JR, Ljung K, Bennett MJ, Owen MR (2016) Dynamic regulation of auxin oxidase and conjugating enzymes AtDAO1 and GH3 modulates auxin homeostasis. PANS 10.1073/pnas.1604458113 Open AccessDAO1pic

Malcolm Bennett and colleagues at CPIB in Nottingham are authors on back-to-back manuscripts in PNAS that investigate the control of auxin metabolism and homeostasis. Both papers focus on the role of the DIOXYGENASE FOR AUXIN OXIDATION 1 (AtDAO1) gene in this process. AtDAO1 is a highly expressed IAA oxidase that, when disrupted, causes significant changes in the steady state levels of oxIAA and IAA conjugates, but not IAA itself, which may explain why the atdao1 mutant has a relatively mild phenotype. AtDAO1, along with the GH3 IAA-conjugating enzymes are auxin-inducible, demonstrating that these proteins play a role in auxin homeostasis that is dependent on the prevailing auxin concentration.

The second paper develops a mathematical model for the interactions between AtDAO1, the GH3 enzymes, the relationship between auxin biosynthesis and conjugation and how these changes occur at different auxin concentrations. In addition they extend this homeostasis model into a multicellular environment demonstrating that the role of AtDAO1 differs across root tissues in a manner that is predicted by the mutant phenotype.

Murray RR, Emblow MS, Hetherington AM, Foster GD (2016) Plant virus infections control stomatal development. Sci Rep. Open Access

Gary Foster and Alistair Hetherington at the University of Bristol are the lead authors on this study that demonstrates that plant viral infections affect stomatal development in both Nicotiana tabacum and Arabidopsis thaliana. In both cases susceptible, but not resistant, plants showed a lower stomatal index (stomatal density / stomatal density+epidermal cell density) whilst the stomatal density was reduced in susceptible Arabidopsis plants. This preliminary study provides evidence for a relationship between viral infection and stomatal development that will undoubtedly lead to many other studies on this topic.

Ooi A, Wong A, Ng TK, Marondedze C, Gehring C, Ooi BS (2016) Growth and development of Arabidopsis thaliana under single-wavelength red and blue laser light. Sci Rep Open Access

This Saudi-Arabia based study includes Claudius Marondedze from the University of Cambridge and uses Arabidopsis as a model to understand mechanisms of growth that are important in the development of indoor horticulture. These experiments involve growing Arabidopsis under high-powered single-wavelength lasers and show that they grow normally from seed to seed. The authors perform a proteomic analysis and show that these plants have lower expression of proteins involved in light and radiation stress. Therefore this study offers an insight into the potential of using this next generation lighting technology for future horticultural applications.

Eremina M, Unterholzner SJ, Rathnayake AI, Castellanos M, Khan M, Kugler KG, May ST, Mayer KF, Rozhon W, Poppenberger B (2016) Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants. PNAS

This German-led study includes GARNet Committee member and NASC Director Sean May and looks into the role of brassinosteroids in the control of freezing tolerance in Arabidopsis. BR-response mutants are hypersensitive to freezing while constitutive BR signaling provides enhanced freezing tolerance. This study shows that this BR effect is mediated via well-known C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR (CBF) proteins but also through CBF-independent signaling. Finally the authors provide a model to explain the role of BR during the response to freezing stress. BRpic

Arabidopsis Research Roundup: September 27th 2016

This weeks Arabidopsis Research Roundup includes an audio description provided by Katja Graumann from the Oxford Brookes Plant Endomembrane Group. Katja is involved in two of this weeks papers, the first of which describes the biology of a novel set of Nuclear Envelope (NE) localised proteins whereas the second is a phylogenetic analysis of a range of known NE-localised proteins. Elsewhere David Salt (CPIB) is the corresponding author on work that investigates the plants response to sulphur while David Twell (Leicester) co-leads a study into regulatory events that occur during early male germline development. Finally Juriaan Ton (Sheffield) is a co-author on a study that looks at the role of NAD in the defence response.

Pawar V, Poulet A, Détourné G, Tatout C, Vanrobays E, Evans DE, Graumann K (2016) A novel family of plant nuclear envelope-associated proteins. J Exp Bot

This study is lead by David Evans and Katja Graumann from the Oxford Brookes Nuclear Envelope (NE) Group and describes a newly discovered family of proteins that are associated with the Nuclear Envelope (NE). These Nuclear Envelope-Associated Proteins (NEAPs) are ubiquitously expressed and localize to the NE through a predicted TM domain. A genetic analysis showed that NEAP proteins are necessary for correct nuclear morphology. They form homodimers and also interact with the SUN1 and SUN2 proteins that also reside at the NE. Interestingly the authors show that NEAP1 interacts with the putative transcription factor AtbZIP18, indicative of a role for these proteins in the regulation of gene expression.

Katja kindly takes a few minutes to provide an audio description of the work that went into this paper.

NEAPpicPoulet A, Probst A, Graumann K, Tatout C, Evans D (2016) Exploring the evolution of the proteins of the plant nuclear envelope. Nucleus

David Evans (Oxford Brookes) is the corresponding author of this UK-French collaboration that uses phylogenetic analysis to investigate the evolution of nuclear envelope proteins throughout higher plants. These include Sad1-Unc84 (SUN) domain, Klarsicht/Anc1/Syne homology (KASH) domain and Crowded Nuclei (CRWN) proteins. In general the number of SUN proteins is conserved throughout higher plants whilst the function of the KASH domain proteins appears to have extended through evolutionary time. Contrary to many historic reports, it has become clear that the plant inner nuclear membrane contains a lamin-like structure and although the proteins proposed to make up this structure in plants (CRWN, NEAPs and KAKU4) can be identified in most plant lineages, they are absent in other eukaryotes. This suggests the factors that maintain nuclear structure convergently evolved a mode of maintaining nuclear structure.

Huang XY, Chao DY, Koprivova A, Danku J, Wirtz M, Müller S, Sandoval FJ, Bauwe H, Roje S, Dilkes B, Hell R, Kopriva S, Salt DE (2016) Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana. PLoS Genet. 12(9):e1006298 Open Access

Current GARNet Chair David Salt (then Aberdeen but recently moved to CPIB in Nottingham) leads this collaboration between UK, US and German researchers that identifies the MORE SULPHUR ACCUMULATION1 (MSA1) protein, which regulates sulphur homeostasis. MSA1 is nuclear localised, is required for S-adenosylmethionine (SAM) production and DNA methylation whilst is essential for the response to sulphur. Therefore the authors show that MSA1 appears to sit at an important control point as the plant responds to sulphur by regulating SAM biosynthesis and genome-wide DNA methylation.

Peters B, Casey J, Aidley J, Zohrab S, Borg M, Twell D, Brownfield L (2016) A cis-regulatory module in the transcription factor DUO1 promoter. Plant Physiol. Open Access

David Twell (University of Leicester) is a co-corresponding author with Lynette Brownfield from the University of Otago in New Zealand. They investigate the DUO POLLEN1 (DUO1) protein that is only expressed in the male germline following the first asymmetric division that segregates the germ cell lineages. Following generation of transgenic reporter lines the authors conclude that expression of the DUO1 gene is controlled at the transcriptional level and so identified a <100bp a cis-element termed the Regulatory region Of DUO1 (ROD1). The Arabidopsis ROD1 could replicate the germline expression pattern when introduced into Medicago and the authors subsequent show that this regulatory module likely has conserved function across dicots. Therefore as the ROD1 is necessary for the specification for the male germline across plant species, it represents one of the earliest regulatory checkpoints during sexual reproduction in dicots.
DUO1Pétriacq P, Ton J, Patrit O, Tcherkez GG, Gakiere B (2016) NAD acts as an integral regulator of multiple defense layers Plant Physiol
http:/​/​dx.​doi.​org/10.1104/pp.16.00780 Open Access
University of Sheffield group leader (and recent ARR audio contributor) Juriaan Ton is an author on this Franco-Australian study into the role of nicotinamide adenine dinucleotide (NAD) as a signalling molecule during the defence response. Previously NAD-overproducing nadC plants have been shown to be more resistant to Pseudomonas syringae and this study extends this analysis to show increased resistance to a broader set of pathogens. Increased NAD induces production of reactive oxygen species (ROS) independent of NADPH oxidase and light metabolism but dependent on mitochondrial respiration. Furthermore, NAD primes the physical aspects of the defence response by increasing callose deposition and pathogen-responsive cell death. Metabolic profiling reveals that the plant responds to NAD similarly to pathogen-associated molecular patterns (PAMPs) and may provide an alternant signalling pathway to enable the plant to responses to pathogen attack. Finally the authors discuss how this signalling crosstalk may define the defence response.

Toolkit for the Gene Editing of Chromosomal Deletions.

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Published on: September 20, 2016

A new manuscript from the lab of Johannes Stuttmann from Halle University describes the generation of a new toolkit for CRISPR-Cas9 genome editing, which they use to produce chromosomal deletions as well as more ‘routine’ point mutations.

This strategy relies upon the use of dual-targeted Cas9 enzymes that, when both nucleases successfully cut, will generate a deletion. Deletion mutations are clearly more effective when attempting to generate a null mutation or in the analysis of non-coding regions of the genome.

This manuscript details the creation of the Dicot Genome Editing (pDGE) vectors that have been developed from the Golden Gate-based plant synthetic biology resources developed by the lab of Sylvestre Marillonnet. This toolkit allows facile creation of binary vectors that contain up to eight guide RNAs (sgRNAs) as well as the required Cas9 nuclease and selectable markers.



In order to test the dose response of using multiple sgRNAs targeted to the same location, a ‘GUS-out-of-frame’ assay was used. The restoration of GUS expression (by errors in NHEJ) was the reporter output, showing that an increase in sgRNAs caused an increase in GUS expression. This indicates that the copy number of a sgRNA might be a limiting factor in a Cas9-mediated gene editing reaction.

This demonstration of plasmid function led to subsequent experiments, using multiple sgRNAs that targeted the same location, aimed at deleting portions of the Arabidopsis or tobacco genomes.

They showed that generation of deletions was possible across a range of targeted loci and designed experiments whereby either a small or larger deletion was possible using the same two sgRNAs. They found that smaller 100bp deletions occured in about 10% of cases whilst larger >5kb fragments were removed less than 1% of the time. Although this indicates that a smaller deletion size is selected for, it goes against previous evidence from animal systems and these authors suggest that it is more likely that the efficacy of sgRNA binding is the most likely contributory factor.

Importantly they found that use of multiple sgRNAs did not increase the chance of off-target effects and the authors speculate that this is unlikely to be a significant problem in plants.

In this manuscript the authors also discuss the efficacy of using different promotors for expression of Cas9 as well as effectiveness of using different target sites.

However ultimately they suggest that additional work is needed to define the best promotors to use and the optimal parameters that will inform target site design. In the latter case they discovered no correlation between the predicted strength of the target site and the actual in vivo effect. However the general rule applies that use of multiple targets to a single locus is preferable to increase the chance of obtaining a knockout, even though the precise nature of that knockout will not be be known without empirical testing.

This new toolkit for CRISPR-Cas mediated gene editing is available from Addgene (Kit #1000000084) or from the host lab and the online manuscript includes a comprehensive Appendix on usage of this set of vectors.

Arabidopsis Research Roundup: September 19th.

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Published on: September 18, 2016

This weeks Arabidopsis Research Roundup includes a study from the University of Warwick investigating the role of the ubiquitin-proteasome system in the defense response. Secondly researchers from Warwick (again), Durham and Rothamsted are involved in a paper that links cell cycle progression to production of endomembranes. Finally are two studies that include researchers from Edinburgh that firstly provide an insight into the non-specific transport of molecules into the phloem and secondly looks at the cellular basis of endosperm breakdown.

The latter study is part of a special issue of the journal Development that focuses on plant science and includes tributes to the late Ian Sussex. This issue contains paper that have been highlighted in the ARR together the summer.

Üstün S, Sheikh A, Gimenez-Ibanez S, Jones AM, Ntoukakis V, Börnke F (2016) The proteasome acts as a hub for plant immunity and is targeted by Pseudomonas type-III effectors Plant Physiology

Open Access

Alex Jones and Vardis Ntoukakis (University of Warwick) are co-authors on this German-led study that investigates the hypothesis that plant pathogens enhance their virulence by targeting the ubiquitin-proteasome system (UPS). The authors show that the UPS is induced upon basal defence and that proteasomal subunit mutants are more sensitive to growth of Pseudomonas species. This indicates that the UPS is involved in defence priming and also establishment of systemic-acquired resistance (SAR). A screen for bacterial effectors that interact with the proteasome yielded four known candidates. Subsequently they show HopM1 interacts with several E3 ligases and proteasome subunits. Therefore this study further demonstrates that the proteasome is a key component of the defence response and might be a potential target for future generation of pathogen resistant plants.

Craddock CP, Adams N, Kroon JT, Bryant FM, Hussey PJ, Kurup S, Eastmond PJ (2016) Cyclin-dependent kinase activity enhances phosphatidylcholine biosynthesis in Arabidopsis by repressing phosphatidic acid phosphohydrolase activity Plant Journal Open Access

This collaborative research between the Universities of Warwick and Durham with Rothamsted Research is led by Peter Eastmond. They investigate the coordinated biogenesis of endomembranes throughout the cell cycle, building on previous work that had demonstrated that disruption of the PHOSPHATIDIC ACID PHOSPHOHYDROLASE (PAH) enzyme caused expansion of the ER. In this work they show PAH expression is dependent on phosphorylation by the cell cycle regulatory CYCLIN-DEPENDENT KINASE A;1 (CDKA;1). Use of a CDKA;1 insensitive versions of PAH results in less endomembrane production and a reduced rate of cell division. This demonstrates that growth of the endomembrane is tightly linked to cell division, a control mechanism that ensures the cell is fully prepared with sufficient endomembranes to support the daughter cells that result from division.

Paultre DS, Gustin MP, Molnar A, Oparka KJ (2016) Lost in transit: long-distance trafficking and phloem unloading of protein signals in Arabidopsis homografts Plant Cell

Karl Oparka (University of Edinburgh) is the corresponding author of this paper that uses micrografting to assess the long-distance movement of GFP-tagged proteins. They found that it took 10 days for GFP-tagged proteins to move from transgenic scions into non-transgenic roots, targeted to either chloroplasts, peroxisomes, actin, or to the nucleus. However, proteins targeted to endoplasmic reticulum or Golgi did not move through the plant. This demonstrates that there is extensive movement of proteins throughout the plant, thus explaining the many macromolecules that can be found in the phloem. However they also some that the recipient roots demonstrate limited movement outward from the phloem, the selective blockage occurring at the plasmodesmata between stele and cortex.

Fourquin C, Beauzamy L, Chamot S, Creff A, Goodrich J, Boudaoud A, Ingram G (2016) Mechanical stress mediated by both endosperm softening and embryo growth underlies endosperm elimination in Arabidopsis seeds Development. 143(18):3300-5.

Justin Goodrich (University of Edinburgh) is a co-author on this study from the lab of Gwyneth Ingram in Lyon that looks in detail at the mechanisms that control the breakdown of the coenocytic endosperm, which is essential for the nourishment of the growing embryo. The programmed cell death of the endosperm is controlled by the basic helix-loop-helix transcription factor ZHOUPI. This study shows that this is not a direct effect but rather occurs via the expression of cell wall-modifying enzymes, which alter the physical properties of the endosperm, enabling its compression as the developing embryo expands.

EURISCO: the EU Plant Genetic Resource Catalogue

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Published on: September 15, 2016

A paper about the ‘EURISCO: The European search catalogue for plant genetic resources’ was recently published in the Nucleic Acids research and outlines the process behind the generation of the resources that can be found at

A vital consideration in the establishment of ‘plant genetic resources for food and agri- culture’ (PGRFA) is in the maintenance of Genebanks that store the genetic information from a particular region. Contrary to some thoughts, Genebanks do much more than converse seed as many are heavily involved in the characterisation of the resources in terms of phenotypic variation with regard disease resistance, response to different environment conditions and yield parameters. Therefore Genebanks contain a valuable source of information that will benefit current and future researchers and breeders.

The European Search Catalogue for Plant Genetic Re- sources (EURISCO) aims to collate PGRFA from 625 Genebank collections that are maintained across Europe. This resource was established in 2001 by a pan-European consortium funded by the EU-project EPGRIS (European Plant Genetic Resources Information Infra- Structure). In 2014 management of this resource passed to Institute of Plant Genetics and Crop Plant Research (IPK) in Germany and took on a more technological basis to act as an umbrella organisation to coordinate the standardised deposition of data of the PGRFA information submitted by National Inventories. Therefore the EURISCO database maintains passport and phenotypic data from collections all across Europe. The largest collections predictably pertain to Arabidopsis, wheat, barley and maize with a particular focus on plants adapted to growth in temperate zones.

The main entry point for this resource is the EURISCO web interface that initially allows a user to search for stocks based on taxonomy, accession, biological status and collecting site. In order to maintain up to date relevance, each National Inventory annually uploads information that is collated from research institutions within their member country. Importantly in this era where the effective management and sharing of data is an important component that follows the generation of data, all the uploaded data is extensively cleansed and checked for consistency, with regard parameters such as plant names and geographical coordinates.

EURISCO provides a central repository for information about the genetic diversity that exists from collaboration collections of germplasm from around Europe. The goal of having a centralised location will hopefully add value to future studies that aim to take advantage of the diversity that exists across the continent whether that is in proposed sequencing or phenotypic studies.

As the tools now exist to mine the genetic diversity that is present in wild populations, EURISCO can be of benefit to researchers interested in this area by maintaining information on over 200K wild varieties, alongside a similar number of landrace accessions.

A historic problem with the sharing phenotypic data is in the usage of different phenotypic descriptors, so it is hoped that EURISCO can aid in efforts to standardise the challenging semantics of phenotypic description by interacting with programs such as the Minimum Information about Plant Phenotyping Experiments (MIAPPE) or CropOntology.

Finally and importantly for the busy researcher, EURISCO helps to deal with national and international legal obligations and commitments with regard the sharing and usage of genetic resources.

EURISCO is an evolving resource that will greatly benefit from demonstratably usage by the research community so please go and check it out!

Arabidopsis Research Roundup: September 13th.

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Published on: September 13, 2016

This addition of the Arabidopsis Research Roundup includes a broad range of research topics. At the cellular level is a study led by Malcolm Bennett (CPIB) that adds a layer of complexity to our understanding of lateral root development whilst Johnathan Napier (Rothamsted) is a co-author on an investigation into the function of fatty acid elongase complexes. At the tissue level John Christie (University of Glasgow) leads a study into the role of light signaling on hypocotyl development and David Salt (CPIB) contributes to the biomaging of ions along the Arabidopsis root. Finally at the population level James Brown (JIC) assess the role of competition between genotypes on population level yield in response to pathogen attack.

Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benkova E, Fukaki H, Brady SM, Scheres B, Péret B, Bennett MJ (2016) Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulating auxin influx carrier LAX3. Development.


Malcolm Bennett (CPIB) is the corresponding author of this study that includes authors from the UK, USA, France, Portugal, The Netherlands, Switzerland, Austria and Japan. This manuscript adds further layer of complexity to our understanding of the factors that promote lateral root development, focussed on the role of the influx carrier LAX3 to concentrate auxin into cell layers overlying lateral root primordia. This study demonstrates that the auxin response factor ARF7 upregulates the LBD29 TF that in turn directly binds the LAX3 promotor. Disrupting the dynamics of wildtype LBD29 binding to the LAX3 promotor phenocopies the lax3 mutant, functionally demonstrating the ARF7-LBD29-LAX3 signalling module.



Morineau C,, Gissot L, Bellec Y, Hematy K, Tellier F, Renne C, Haslam R, Beaudoin F, Napier J, Faure JD (2016) Dual Fatty Acid Elongase Complex Interactions in Arabidopsis PLoS One. http:/​/​dx.​doi.​org/10.1371/journal.pone.0160631

Open Access

This French-led study includes Johnathan Napier (Rothamsted) as a co-author and looks at the role of Very long chain fatty acids (VLCFAs) in plant development. Novel factors involved in the biosynthesis or function of VLCFA were identified following a screen in yeast and genetic studies using Arabidopsis mutants. Their plant work focuses on the functional interaction between the dehydratase genes PASTICCINO2 (PAS2) and PROTEIN TYROSIN PHOSPHATASE-LIKE (PTPLA), which are both involved in fatty acid (FA) elongation. These genes have specific and distinct expression domains within the root suggesting the activity of two independent cellular FA elongase complexes. This was confirmed after ectopic expression of PAS2 and PTPLA in the same cell files.


Sullivan S, Takemiya A, Kharshiing E, Cloix C, Shimazaki KI, Christie JM (2016) Functional Characterisation of Arabidopsis Phototropin 1 in the Hypocotyl Apex. Plant Journal http:/​/​dx.​doi.​org/10.1111/tpj.13313

Open Access

John Christie (University of Glasgow) is the corresponding author on this study that investigates the role of the blue-light receptor Phototropin (PHOT1) in the apex of the Arabidopsis Hypocotyl. The site of light perception is in the hypocotyl apex yet PHOT1 is expressed throughout the organ. The authors expressed PHOT1-GFP in the hypocotyl apex in a phot1 mutant and showed in fact that regions outside this expression domain were needed to transmit various aspects of the light signaling response. The authors also show that the interaction between PHOT1 and its signaling partner Non-Phototropic Hypocotyl 3 (NPH3) occurs more prominently in the basal hypocotyl. This demonstrates that the site of light perception does not only occur in the apex as previously thought following more crude decapitation experiments.


Persson DP, Chen A, Aarts MG, Salt DE, Schjoerring JK, Husted S (2016) Multi-element bioimaging of Arabidopsis thaliana roots. Plant Physiology

http:/​/​dx.​doi.​org/10.1104/pp.16.00770 Open Access
GARNet chairman David Salt (University of Nottingham) is a co-author on this Danish-led study that uses Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) to identify the distribution of ions in the Arabidopsis root. This proof-of-concept study demonstrates the power of this technique by showing that a Arabidopsis mutant that is unable to chelate metals accumulates substantially more zinc than in wildtype roots. In addition they were able to show tissue-specific differences in the distribution of iron in epidermal and cortical cells. Therefore this technique offers an outstanding opportunity to study ion distribution in roots, which can then be integarted with the broad range of genetic tools available in Arabidopsis.
Ion_PicCreissen HE, Jorgensen TH, Brown JK (2016) Impact of disease on diversity and productivity of plant populations. Funct Ecology

http:/​/​dx.​doi.​org/10.1111/1365-2435.12552 Open Access

James Brown (John Innes Centre) is corresponding author on this ecological study at the population level of the disease resistance of different Arabidopsis genotypes. Plants were infected with either oomycete Hyaloperonospora arabidopsidis and Turnip yellows virus and their subsequent fitness and competitive ability were determined by phenotypic measurements such as seed mass, rosette size and flowering time. As expected, reduction in competitive ability of suspectible genotypes associated with an increase in competitive ability of resistant genotypes. Interestingly in experiments with the oomycete the highest overall yield was shown from mixtures of two weakly competing genotypes demonstrating buffering on the population level. This is lost when genotypes with wide competitive differences are grown together. However the authors caution that the specific outcomes of competive interactions cannot be generalised due to differences in the type of pathogen and host genotype.

Arabidopsis Research Roundup: August 26th

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Published on: August 26, 2016

This weeks Arabidopsis Research Roundup includes three papers across a wide range of topics. Firstly is a widely-reported study, described here with an audio description by Nik Cunniffe and Sanjie Ziang, of the evolutionary relationship between viral infection, pollinator attraction, plant fertility and miRNA-regulated gene expression. Secondly, Gordon Simpson is a co-author on a paper that has elucidated the crystal structure of the FPA proteins and finally Gareth Jenkins leads an investigation into the relationship between UV light, the UVR8 protein and histone modifications.

Groen SC, Jiang S, Murphy AM, Cunniffe NJ, Westwood JH, Davey MP, Bruce TJ, Caulfield JC, Furzer OJ, Reed A, Robinson SI, Miller E, Davis CN, Pickett JA, Whitney HM, Glover BJ, Carr JP (2016) Virus Infection of Plants Alters Pollinator Preference: A Payback for Susceptible Hosts? PLoS Pathog. 12(8):e1005790


Open Access
This pan-UK collaboration is led by John Carr, Beverly Glover and Nik Cunniffe at the University of Cambridge and has received wide attention in the general press. Nik Cunniffe also kindly provides an audio description of this work that looked into the effect of viral infection on the attraction of pollinators. The authors used GC-MS to look at the volatiles produced in virally infected Arabidopsis and tomato plants, showing that infection can alter the foraging behavior of bumblebees. Mutational analysis of both cucumber mosaic virus (CMV) and Arabidopsis showed that the microRNA pathway is involved in regulating the emission of these pollinator-perceivable volatiles. When virus-infected tomato plants were not pollinated there was a clear reduction in seed yield, indicating that the plant requires the volatile production following viral infection to attract pollinators, leading to reproductive success. Importantly the authors model the possible trade-off between viral infection and reproductive success in the wild, which might oppose the strong selective pressure for the establishment of disease-resistance genes. The authors speculate that this is a co-beneficial relationship for both virus and plant.

Nick Cunniffe and Sanjie Jiang kindly provide an audio description of this work.


Zhang Y, Rataj K, Simpson GG, Tong L (2016) Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA PLoS One 11(8):e0160694


Open Access

Gordon Simpson (University of Dundee) in a co-author on this US-led study that has elucidated the crystal structure of the SPOC domain of the FPA floral regulator protein. FPA contains a N-terminal RNA recognition motif and a C-terminal SPEN paralog and ortholog C-terminal (SPOC) domain. This SPOC domain is highly conserved throughout plant species and this crystal structure is an important development in our understanding of the regulation of RNA 3’-end formation and how much the plant SPOC domains compare with an equivalent from metazoans.


Velanis CN, Herzyk P, Jenkins GI (2016) Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification Plant Mol Biol.


Open Access

Gareth Jenkins (Glasgow) leads this study that continues his groups work on the Arabidopsis UVR8 photoreceptor. They show that UV-B exposure increases histone lysine acetylation on UVR8-regulated genes in a UVR8 dependent manner. In fact all of the histone enrichments throughout the genome following UV-B required UVR8 activity. However the authors could find no direct interaction between UVR8 and the known enzymes involved in light-mediated histone modification indicating that UVR8 either interacts with a novel set of proteins or the UVR8 effect is mediated via a currently unknown signaling intermediate.

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