Arabidopsis Research Roundup: March 31st.

This bumper edition of the Arabidopsis Research Roundup includes a wide range of research topics. Firstly Mike Roberts leads a study that adds another layer of complexity to our understanding of the factors that control seed dormancy. Secondly a paper from Ottoline Leyser’s lab at SLCU provides more details regarding the role of BRC1 during shoot branching. Next is a paper that continues David Salt’s collaborative work that aims to understand how the root endodermal barrier influences nutrient uptake. Fourthly is work from Bristol that looks at the interaction between viral infection, the structure of the leaf surface and the polarization of reflected light. The fifth paper features a wide collaboration from the Sainsbury lab in Norwich and aims to more fully understand the factors that lead to non-host infection by Phytophthora infestans. The penultimate paper looks at the interaction of aldolase enzymes with the plant actin cytoskeleton and the final paper brings us full circle back to seed dormancy where researchers from University of Warwick investigate the link between this complex growth response and the circadian clock.

Singh P, Dave A, Vaistij FE, Worrall D, Holroyd GH, Wells JG, Kaminski F, Graham IA, Roberts MR (2017) Jasmonic acid-dependent regulation of seed dormancy following maternal herbivory in Arabidopsis. New Phytol http:/​/​dx.​doi.​org/10.1111/nph.14525

Taken from:

Open Access

Mike Roberts (University of Lancaster) kindly provides an audio description of this paper on the GARNet YouTube channel, explaining that, in collaboration with Ian Graham at the University of York, they have identified a new control mechanism that links jasmonic acid, herbivory and seed dormancy. ABA and GA are known to be important hormones in the control of seed dormancy but this study adds complexity to this story by showing that following herbivory (or leaf wounding), the level of JA increases within Arabidopsis seeds. Perhaps counter-intuitively, in the following generation this leads to a reduction in dormancy, causing seed to germinate sooner than those from non-predated parents. The authors show that this is due to an increase in JA within seeds that importantly also alters sensitivity to ABA. Unlike transgenerational defence priming that acts through a epigenetic mechanism and persists for multiple generations , this study shows that the JA effect on seeds is a more direct response. Ultimately the mechanism in which parents prepare their offspring for subsequent generations is a complex trade off between multiple sources of predation and pathogenesis, environmental factors as well as through the effect of interacting hormone signaling pathways.

Seale M, Bennett T, Leyser O (2017) BRC1 expression regulates bud activation potential, but is not necessary or sufficient for bud growth inhibition in Arabidopsis. Development http:/​/​dx.​doi.​org/10.1242/dev.145649 Open Access

This is the latest contribution from Ottoline Leyser’s lab that looks into the hormonal control of shoot branching. A key determinant of this process is the transcription factor, BRANCHED1 (BRC1) yet this study shows that under certain conditions, in this case with varied amount of strigolactone, the controlling effect of BRC1 expression levels can be mitigated. The authors provide evidence for a mechanism for branching control that involves the coordinated activity of BRC1 and an auxin-transport mechanism, both of which are influenced by a separate strigolactone-mediated signaling pathway.

Li B, Kamiya T, Kalmbach L, Yamagami M, Yamaguchi K, Shigenobu S, Sawa S, Danku JM, Salt DE, Geldner N, Fujiwara T (2017) Role of LOTR1 in Nutrient Transport through Organization of Spatial Distribution of Root Endodermal Barriers. Current Biology


Former GARNet chairman David Salt is a co-author on this paper that is lead by Japanese and Swiss colleagues and continues his work on the development of the casparian strip. These rings of lignin polymers are deposited within root endodermal cells and play a key role in the movement of water and nutrients into the vascular tissue. Suberin lamellae have a similar function and surround endodermal cells, likely acting as a barrier to apoplastic movement. This paper documents the identification of the Tolkienesquely-named LOTR1, which is essential for casparian strip formation. Lotr1 mutants show disrupted casparian strips, ectopic suberization and reduced calcium accumulation in the shoot. Further analysis demonstrates that it is this suberized layer substitutes for the CS in regions of lateral root emergence. Utliamtely they show that the relationship between suberization of the endodermal layer is a key determinant of calcium movement into the root and then around the rest of the plant.

Maxwell DJ, Partridge JC, Roberts NW, Boonham N, Foster GD (2017) The effects of surface structure mutations in Arabidopsis thaliana on the polarization of reflections from virus-infected leaves. PLoS One

http:/​/​dx.​doi.​org/10.1371/journal.pone.0174014.g003 Open Access

Gary Foster (University of Bristol) leads this study that continues his labs work on the effect that viral infection has on light polarization when reflected off leaves. This attribute is important to attract insect predators, which in turn increase the possibility of successful viral transmission. Light polarization is affected by structures on the leaf surface such as trichomes or the makeup of the waxy cuticle. Here the authors show that the cer5 wax synthesis mutant alters the polarization of light following infection with Turnip vein clearing virus (TVCV) but not following infection with Cucumber mosaic virus (CMV). The paper provides no mechanism for this difference but the authors do show that leaf viral titre is equivalent in these mutants and therefore speculate that these changes might influence transmission of each virus by a different insect carrier that in turn responses to different patterns of polarized light.

Prince DC, Rallapalli G, Xu D, Schoonbeek HJ, Çevik V,, Asai S,, Kemen E,, Cruz-Mireles N, Kemen A,, Belhaj K, Schornack S,, Kamoun S, Holub EB, Halkier BA, Jones JD (2017) Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana. BMC Biol. 

http:/​/​dx.​doi.​org/10.1186/s12915-017-0360-z  Open Access

This paper is a wide collaboration that features many colleagues from the Sainsbury lab in Norwich. Wildtype Arabidopsis plants are suspectible to Phytophthora infestans only after earlier infection with Albugo laibachii yet the molecular explanation of this complex interaction between plant and microbes remained opaque. This study demonstrates that Albugo infection alters the levels of a set of tryptophan-derived antimicrobial compounds, which were then found to be relevant for infection with P.infestans. This shows that these antimicrobial compounds might be key for the general maintenance of non-host resistance and might provide important information to aid future strategies to improve food security by reducing biomass loss due to plant pathogens.

Garagounis C, Kostaki KI, Hawkins TJ, Cummins I, Fricker MD, Hussey PJ, Hetherington AM2, Sweetlove LJ (2017) Microcompartmentation of cytosolic aldolase by interaction with the actin cytoskeleton in Arabidopsis. J Exp Bot.


This collaboration between the Universities of Oxford, Bristol and Durham looks into the functional role that molecular microcompartments play in the workings of a cell. Animal models have shown that certain aldolase enzymes are able to function as actin-bundling proteins and so this study focuses on a major plant cytosolic aldolase, FBA8, which is predicted to have two actin binding sites. Although the authors could not detect co-localisation of FBA8-RFP with the actin cytoskeleton they provide in vitro evidence that FBA8 can functionally interact with F-actin. In addition in fba8 mutants there is altered arrangement of actin filaments in guard cells that concomitantly results in a reduced rate of stomatal closure. Therefore these findings leads the authors to propose that FBA8 is able to subtly interact with actin in vivo, evidenced by some FRET-FLIM experiments, and that this may modulate actin dependent cell responses.

Footitt S, Ölcer-Footitt H, Hambidge AJ, Finch-Savage WE (2017) A laboratory simulation of Arabidopsis seed dormancy cycling provides new insight into its regulation by clock genes and the dormancy-related genes DOG1, MFT, CIPK23 and PHYA. Plant Cell Environ http:/​/​dx.​doi.​org/10.1111/pce.12940

William Savage-Finch (University of Warwick) is the corresponding author on this paper that investigates mechanisms that control seed dormancy, which has been built from the analysis of a variety of genetic and environmental factors. They test their predictions by testing a range of mutants in both known dormancy related genes and in the function of the circadian clock. This provides a link between the circadian cycle and the daily variation in the level of seed dormancy in Arabidopsis.

Arabidopsis Research Roundup: January 11th

The first Arabidopsis Research Roundup of 2017 includes a wide range of studies that use our favourite model organism.

Firstly Kerry Franklin (University of Bristol) is the corresponding author on a paper that describes the complex interaction between the responses to sunlight and heat. Secondly Paul Dupree (University of Cambridge) leads a study that defines the important structural relationship between xylan and cellulose. Thirdly members of Gos Micklem’s group in Cambridge are part of the Araport team that present their ThaleMine tool.

Richard Napier (University of Warwick) is a co-author on the fourth paper that introduces a new chemical tool for study of the auxin response. The penultimate paper includes Matthew Terry (University of Southampton) on a paper that investigates the role of a Fe-S-containing protein cluster in chlorophyll biosynthesis and finally there is a methods paper from Stefanie Rosa in Caroline Dean’s lab at the John Innes Centre that describes the use of FISH to detect single molecules of RNA.

Hayes S, Sharma A, Fraser DP, Trevisan M, Cragg-Barber CK, Tavridou E, Fankhauser C, Jenkins GI, Franklin KA (2016) UV-B Perceived by the UVR8 Photoreceptor Inhibits Plant Thermomorphogenesis. Current Biology http:/​/​dx.​doi.​org/10.1016/j.cub.2016.11.004

Open Access

This collaboration between the research groups of Kerry Franklin (University of Bristol) and Gareth Jenkins (University of Glasgow) looks at how the perception of UV-B light inhibits the morphological changes that occur in response to increased temperatures (thermomorphogenesis). This response includes induced hypocotyl elongation, which is mediated via PIF4 and various players in the auxin response. Interestingly the authors show that UV-B light perceived by UVR8 attenautes this response by preventing PIF4 abundance and by stabilising the the bHLH protein LONG HYPOCOTYL IN FAR RED (HFR1) protein. These results suggest that there exists a precise mechanism for fine-tuning the growth responses that occur in sunlight that would usually include both increased temperature and UV-B irradiation.

Simmons TJ, Mortimer JC, Bernardinelli OD, Pöppler AC, Brown SP, deAzevedo ER, Dupree R, Dupree P (2016) Folding of xylan onto cellulose fibrils in plant cell walls revealed by solid-state NMR. Nat Commun.

http:/​/​dx.​doi.​org/10.1038/ncomms13902 Open Access
In this paper Paul Dupree (University Cambridge) collaborates both with colleagues in Spain and with his father Ray, who is a physicist at the University of Warwick. They use NMR to perform a structural analysis of xylan, which is the most prevalent non-cellulosic polysaccharide in the cell wall matrix and binds to cellulose microfibrils. Whereas in solution xylan forms a threefold helical screw, it flattens into a twofold helical screw ribbon to closely bind to cellulose when in the cell wall. They used the cellulose-deficient Arabidopsis irx3 mutant to show that the xylan two-fold screw confirmation breaks down when it cannot bind cellulose. The authors state that this finding has important implications in our understanding of the formation of the cell wall and perhaps more importantly how it might be broken down during attempts to maximise economic usages of plant biomass.

A local Cambridge newspaper reported that this finding could ‘pave the way for wooden skyscrapers’

Krishnakumar V, Contrino S, Cheng CY, Belyaeva I, Ferlanti ES, Miller JR, Vaughn MW, Micklem G, Town CD, Chan AP (2016) ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery. Plant Cell Physiol http:/​/​dx.​doi.​org/10.1093/pcp/pcw200 Open Access

This paper is presented by the Araport team, which is based in the USA but includes representatives from Gos Micklem’s lab in University of Cambridge. They outline the functionality of the ThaleMine data warehouse which is an important component of the tools included on Araport ( ThaleMine collects a wide variety of data from public datasets and presents it in a easy-to-interrogate form, facilitating the experiments of both lab-based researchers or bioinformaticians. This tool is build upon the InterMine software framework, which has been widely adopted across other model organisms.

Chris Town and Sergio Contrino provided a hands-on workshop describing the tools on Araport in last year GARNet2016 meeting and their workshop materials can be downloaded here.

Steenackers WJ, Klíma P, Quareshy M, Cesarino I, Kumpf RP, Corneillie S, Araújo P, Viaene T, Goeminne G, Nowack MK, Ljung K, Friml J, Blakeslee JJ, Novák O, Zažímalová E, Napier RM, Boerjan WA, Vanholme B (2016) cis-cinnamic acid is a novel, natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiol. http:/​/​dx.​doi.​org/pp.00943.2016 Open Access
This pan-european collaboration includes members of Richard Napier’s lab at the University of Warwick. They outline the activity of a novel inhibitor of auxin efflux transport called cis-cinnamic acid (c-CA). When c-CA is applied to growth media plants appears to exhibit an auxin-response phenotype yet these experiments show that c-CA is neither an auxin or anti-auxin and in fact blocks local auxin efflux, thus causing buildup of cellular auxin. This effect does not occur with t-CA showing specificity for c-CA and it does not affect long distance auxin transport, which occurs through the phloem. Therefore this paper presents a new pharamolgical tool for the study of in planta auxin transport and homeostasis.

Hu X, Page MT, Sumida A, Tanaka A, Terry MJ, Tanaka R (2016) The iron-sulfur cluster biosynthesis protein SUFB is required for chlorophyll synthesis, but not phytochrome signaling. Plant J.


Matthew Terry and Mike Page (University of Southampton) are co-authors on this Japanese-led study that investigates the function of the SUFB subunit of the SUFBCD iron-sulfur cluster. These Fe-S protein clusters play roles in many metabolic processes and the SUFB mutant hmc1 exhibits a defect in chlorophyll biosynthesis due to an accumulation of Mg-containing biosynthetic intermediates. In addition both SUFC- and SUFD-deficient RNAi lines accumulated the same Mg intermediate indicating that the SUFBCD cluster is responsible for this step necessary for chlorophyll production.

Duncan S, Olsson TS, Hartley M, Dean C, Rosa S (2016) A method for detecting single mRNA molecules in Arabidopsis thaliana. Plant Methods. http:/​/​dx.​doi.​org/10.1186/s13007-016-0114-x

Open Access
This paper from is lead by Stefanie Rosa in Caroline Dean’s lab at the John Innes Centre describes a novel method for imaging single molecules of RNA by smFISH. They analyse the localisation of both nascent and mature mRNAs, allowing for analysis of the location of RNA processing and translation.<

Arabidopsis Research Roundup: May 5th

There are a bumper crop of papers in this edition of the Arabidopsis Research Roundup. First from the University of Manchester is a paper that identifies a protein involved in plant programmed cell death. Secondly are two papers from the University of Bristol that highlight the role of viruses in the reflectivity of plant leaves and an assessment of the growth parameters of Arabidopsis on different soil-types. Thirdly are three papers from University of Edinburgh that either use CRISPR-Cas technology to develop virus-research plants, investigate the relationship between photoperiod and metabolism or present a method for assessment of protein S-nitrosylation. Fourthly is a paper that includes a contribution from the University of Leeds that investigates the evolutionary and functional relationship of the WOX gene family. Finally is a study that highlights the role of the AUGMIN complex during microtubule activity that includes a contribution from the University of Leicester.

In addition, although not involving Arabidopsis, we should mention an exciting study from Gerben van Ooijen (Edinburgh) that has discovered a conserved circadian mechanism based on magnesium rhythms that is linked to energy expenditure.

Ge Y, Cai YM, Bonneau L, Rotari V, Danon A, McKenzie EA, McLellan H, Mach L, Gallois P (2016) Inhibition of cathepsin B by caspase-3 inhibitors blocks programmed cell death in Arabidopsis. Cell Death Differ. Open Access

The corresponding author of this paper is Patrick Gallois from the University of Manchester and includes contributions from Hazel McLellan in Dundee almongside Chinese and Austrian collaborators. This study investigates the role of caspase proteins on control of programmed cell death in plants. This research area has been hindered by the apparent lack of plant caspase orthologues despite pharmacological evidence that proteins with caspase activity are active in plants. The authors use a labeled caspase-3 inhibitor to identify the Arabidopsis Cathepsin B3 (AtCathB3) protein as having caspase activity, which was verified using recombinant proteins during in vitro enzyme assays. AtCathepsinB1,2,3 triple mutant plants demonstrate a reduction in PCD induced by different stresses and explains why caspase inhibitors are effective tools for studying PCD in plants. The core Cathepsin B protein is evolutionarily conserved suggesting that an ancestral pathway exists that controls PCD, the details of which require further study.

Maxwell DJ, Partridge JC, Roberts NW, Boonham N, Foster GD (2016) The Effects of Plant Virus Infection on Polarization Reflection from Leaves. PLoS One. 11(4):e0152836 10.1371/journal.pone.0152836 Open Access

Gary Foster’s research group at the University of Bristol collaborate with others at the University of York and in Australia for this study that investigates how plant viruses may modify gene expression to benefit their own transmission. They show that Potato virus Y and Cucumber mosaic virus (CMW), which both are transmitted by aphids, significantly reduce the amount of polarised light that is reflected from abaxial leaf surfaces of tobacco plants particularly when compared to the effects caused by non-insect vectored viruses. However this effect was not shown in Arabidopsis leaves infected by a variety of differently transmitted viruses. Interestingly ECERIFERUM6 (CER6) transcripts accumulate to higher levels following infection with insect vectored viruses and as this gene is involved in cuticle wax synthesis the authors suggest that induced changes in cuticle composition might be key in understanding how viruses encourage predation by their insect vectors. Finally the authors discuss the overall adaptive significance of these results.

Drake T, Keating M, Summers R, Yochikawa A, Pitman T, Dodd AN (2016) The Cultivation of Arabidopsis for Experimental Research Using Commercially Available Peat-Based and Peat-Free Growing Media. PLoS One. 11(4):e0153625 10.1371/journal.pone.0153625 Open AccessPeatPic

GARNet committee member Anthony Dodd, also from the University of Bristol, leads this study into the growth of Arabidopsis on peat-free media, which was motivated by the unsustainable use of peat-based composts. They found that biomass accumulation and seed yield were reduced on peat-free media and that some types of this media was more suspectible to fungal contamination. Overall vegetative phenotypic parameters were similar between plants grown on peat-based or peat-free media, indicating that this type of media will be appropriate for future analysis. However the seed yield was usually reduced, indicating that experiments looking at post-phase change phenotypes might not be as comparable between plants growth on media with different amount of peat.

Pyott DE, Sheehan E, Molnar A (2016) Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants Mol Plant Pathol.

Attila Molnar (Edinburgh) is the corresponding author on this study that uses the transformative technology CRISPR/Cas9 to engineer Arabidopsis plants that are resistant to potyvirus infection. This is achieved by targeting the genes encoding the translation initiation factor eIF(iso)4E that had been previously identified as being critical for viral establishment. Importantly they subsequently selected transgene-free plants that have no phenotypic changes when compared to wildtype growth under standard conditions. As the potyvirus Turnip Mosaic Virus is an important pathogen for vegetable crops this is potentially an extremely powerful technique for generating virus-resistance food crops.

Flis A, Sulpice R, Seaton DD, Ivakov AA, Liput M, Abel C, Millar AJ, Stitt M (2016) Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis Plant Cell Environ.

This German–led study aims to connect the expression of photoperiod-length responsive circadian clock-regulated genes with those involved in metabolic processes such as starch degradation and includes a contribution from Professor Andrew Miller from the Edinburgh SynthSys Centre. The authors assess global gene expression by transcript profiling at photoperiods ranging from 4-18 hours and found that changes in transcript abundance at dawn throughout these photoperiods were as large as changes seen in individual experiments when comparing dawn and dusk. These complex interactions revealed coordinated regulation of key metabolic processes and begins to demonstrate how metabolism is linked to photoperiod.

Homem RA, Le Bihan T, Yu M, Loake GJ (2016) Identification of S-Nitrosothiols by the Sequential Cysteine Blocking Technique Methods Mol Biol. 1424:163-74.

This paper from the lab of Gary Loake (Edinburgh) describes the methods they use to investigate the role of protein S-nitrosylation in the immune responses of Arabidopsis. These are based on a modification of the biotin-switch technique, which they term sequential cysteine blocking.

Dolzblasz A, Nardmann J, Clerici E, Causier B, van der Graaff E, Chen J, Davies B, Werr W, Laux T (2016) Stem cell regulation by Arabidopsis WOX genes Mol Plant. S1674-2052(16)30029-6

This German-led study includes work from the lab of Brendan Davies at the University of Leeds and investigates the role of the WUSCHEL-RELATED HOMEOBOX (WOX) transcription factor gene family during stem cell development and maintenance. Most members of the WUS-clade can largely substitute for WUSCHEL activity in the shoot meristem, which is absolutely dependent on a conserved WUS-box motif that is critical for the interaction with TOPLESS co-repressors. In contrast to the WUS clade, the WOX13 and WOX9 clades cannot substitute for WUS activity. The indicates that WOX control of shoot and floral meristem relies on certain currently not-fully-understood attributes of the WUS-clade of proteins.

Oh SA, Jeon J, Park HJ, Grini PE, Twell D, Park SK (2016) Analysis of gemini pollen 3 mutant suggests a broad function of AUGMIN in microtubule organization during sexual reproduction in Arabidopsis Plant J.

David Twell (Leicester) is an author on his Korean-led study that reports on the identification of the new gem3 mutant, which displays defects in gametophytic development. Mutant plants exhibits disrupted cell division during male meiosis, at pollen mitosis I and throughout female gametogenesis. Gem3 is a hypomorphic allele of the AUGMIN subunit 6 gene, which is a component of Augmin complex responsible for microtubule (MT) nucleation in acentrosomal cells. In the gem3 mutant, the authors show that MT arrays are incorrectly distributed, likely causing the gametophyte-specific phenotypes and demonstrating a broad role for the augmin complex during sexual reproduction in flowering plants

Arabidopsis Research Roundup: March 4th

There are six articles in this weeks Arabidopsis Research Roundup that bridge a diverse range of topics. Firstly lead author Deirdre McLachlan provides an audio description of a study that investigates the role of triacylglycerol breakdown in stomatal signaling. Secondly is a study that assesses the role of a Rab GTPase in control of anisotropic cell growth. The third and fourth papers looks into the defence response, focused on either JA or nitric oxide signaling. Finally are two papers that look into the response of Arabidopsis seedlings to growth on either arsenic or cadmium.

McLachlan DH, Lan J, Geilfus CM, Dodd AN, Larson T, Baker A, Hõrak H, Kollist H, He Z, Graham I, Mickelbart MV, Hetherington AM The Breakdown of Stored Triacylglycerols Is Required during Light-Induced Stomatal Opening Current Biology Open Access
Slide 1
The control of stomatal opening is a key environmental response to changes in CO2 levels and water availability. This study, led by Alistair Hetherington (Bristol), demonstrates that triacylglycerols (TAGs), contained in lipid droplets (LD), are critical for light-induced stomatal opening. Following illumination, the number of LDs are reduced through the β-oxidation pathway, a response that requires blue-light receptors. The authors postulate that a reduction in ATP-availability due to delayed fatty acid breakdown contributed to the stomatal phenotype. The lack of available ATP was confirmed following analysis of the activity of a plasma membrane H+-ATPase. Overall the authors suggest that the light-induced breakdown of TAG contributes to an evolutionarily conserved signaling pathway that controls stomatal opening therefore playing a key role in environmental adaptation.

The lead author of this study, Deidre McLachlan kindly provides a brief audio description of this paper.

During our discussion Deidre mentioned some related work that links blue-light signaling and starch degradation during stomatal opening that was included in a recent ARR.


Kirchhelle C, Chow CM, Foucart C, Neto H, Stierhof YD, Kalde M, Walton C, Fricker M, Smith RS, Jérusalem A, Irani N, Moore I (2016) The Specification of Geometric Edges by a Plant Rab GTPase Is an Essential Cell-Patterning Principle During Organogenesis in Arabidopsis. Developmental Cell 36(4):386-400 Open Access
Ian Moore (Oxford) is the corresponding author on this UK-German collaboration that investigates the role of a Rab GTPase in pattern formation during organogenesis. It is known that the endomembrane system controls the asymmetric distribution of cargoes to different ‘geometric edges’ of a plant cell, establishing biochemically distinct domains that are important for anisotropic growth. This study identifies a new type of membrane vesicle that accumulates specifically along geometric edges and that contains the RAB-A5c protein which, when inhibited, distorts the geometry of cells in subsequently formed lateral organs (in this case, lateral roots). Interestingly this effect is independent of changes to general endomembrane trafficking. The precise mechanism of RAB-A5c activity is unknown but loss of its activity reduces cell wall stiffness at domain-specific locations, therefore perturbing cell growth in those directions. Therefore this study provides interesting insight into fundamental mechanisms that control the growth of cells in a developing organ.

Thatcher LF, Cevik V, Grant M, Zhai B, Jones JD, Manners JM, Kazan K (2016) Characterization of a JAZ7 activation-tagged Arabidopsis mutant with increased susceptibility to the fungal pathogen Fusarium oxysporum J Exp Bot. Open Access

Jonathan Jones (TSL) and Murray Grant (Exeter) are collaborators on this research that investigates the role of jasmonic acid signaling in plant resistance to the fungal pathogen Fusarium oxysporum. In this study they show that the JASMONATE ZIM-domain7 (JAZ7) gene is induced by Fusarium oxysporum and that the jaz7-1D mutant has increased suspectibility to infection. This genotype has constitutive JAZ7 expression and also demonstrates sensitivity to a bacterial pathogen. To cause alterations in gene expression, the JAZ7 protein interacts with a range of transcriptional activators and repressors. The authors postulate that in wildtype plants JAZ7 represses the JA-transcriptional network through its interaction with the co-repressor TOPLESS protein and that in the jaz7-1D plants this response network is hyper-activated leading to an inappropriately high response to pathogen attack.

Yun BW, Skelly MJ, Yin M, Yu M, Mun BG, Lee SU, Hussain A, Spoel SH, Loake GJ (2016) Nitric oxide and S-nitrosoglutathione function additively during plant immunity. New Phytol.

Gary Loake and GARNet Advisory board member Steven Spoel (Edinburgh) are the leaders of this UK-Korean collaboration that studies the role of Nitric Oxide (NO) in the plant defence response. NO often undergoes S-nitrosylation to produce S-nitrosothiol (SNO), which is important for its bioactivity. This reaction involves the S-nitrosoglutathione reductase 1 (GSNOR1) enzyme, which serves to turnover the NO donor, S-nitrosoglutathione (GSNO). In this study the authors investigate mutant plants that accumulate NO and some a reduction in the basal defence response due to a reduction in salicylic acid (SA) signaling. This response was not rescued by the overexpression of GSNOR1 even though this was able to reduce phenotypes resulting from SNO accumulation. Mutant plants that have increased NO accumulation but lower activity of GSNOR1, so therefore an increased ratio of NO:SNO, were more suspectible to growth of bacterial pathogens. The authors conclude that the relationship between NO and GSNO is critically for plant immunity and development.

Lindsay ER, Maathuis FJ (2016) Arabidopsis thaliana NIP7;1 is Involved in Tissue Arsenic Distribution and Tolerance in Response to Arsenate FEBS Lett.

Francois Maathuis (York) is the corresponding author of this study that investigates the role of the Arabidopsis aquaglyceroporin NIP7;1 in the uptake of different chemical forms of arsenic. Mutant nip7;1 plants improved the tolerance of arsenic by reducing uptake of the chemical. This is the first demonstration for the role of a NIP transporter in the response to arsenic and highlights the possibility of focussing on these proteins as a target for breeding or genetically-modifying tolerance to this toxic metal.

Wang H, He L, Song J, Cui W, Zhang Y, Jia C, Francis D, Rogers HJ, Sun L, Tai P, Hui X, Yang Y, Liu W (2016) Cadmium-induced genomic instability in Arabidopsis: Molecular toxicological biomarkers for early diagnosis of cadmium stress Chemosphere 150:258-265

Hilary Rodgers (Cardiff) is the sole UK representative on this Chinese study that has developed screening parameters to evaluate the growth of plants on cadmium. The study uses microsatellite instability (MSI) analysis, random-amplified polymorphic DNA (RAPD), and methylation-sensitive arbitrarily primed PCR (MSAP-PCR) to define a range of genomic alterations that occurred after growth of Arabidopsis plants across a range of concentrations of cadmium. They conclude that analysis of genomic methylation polymorphisms were the most sensitive biomarkers to diagnosis early cadmium stress in these plants and provide important insights for future biomonitoring strategies.

Arabidopsis Research Roundup: October 20th

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Published on: October 20, 2015

There are just three research papers in this weeks Arabidopsis Roundup but they each represent important projects from established groups. Firstly is a significant output from the Edinburgh SynthSys Centre that documents their analysis of the Arabidopsis circadian clock. Secondly an international collaborative effort looks into the molecular signaling pathways that control the physiological response to increasing CO2 levels and thirdly a paper that uncovers a novel plant-specific molecular mechanism that controls the biogenesis of certain siRNAs. Finally we highlight a major review concerning the importance of Arabidopsis research over the past 50 years.

Flis A, Fernández AP, Zielinski T, Mengin V, Sulpice R, Stratford K, Hume A, Pokhilko A, Southern MM, Seaton DD, McWatters HG, Stitt M, Halliday KJ, Millar AJ (2015) Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure. Open Biol. 5(10). pii: 150042.

This study of the Arabidopsis circadian clock, impressive in its breadth, is led by faculty members from the University of Edinburgh SynthSys Synthetic Biology Centre. The team measured RNA profiles of clock genes in plants grown with or without exogenous sucrose or from wildtype or mutant soil growth plants. They found surprisingly robust patterns of expression together with some novel genetic behaviours. In addition they discovered major differences in the absolute expression of certain clock genes, ranging from 50 up to 1500 copies/ cell. Importantly this information is freely-available within the BioDare repository and it is hoped that this will benefit future attempts at modeling the circadian clock.

Chater C, Peng K, Movahedi M, Dunn JA, Walker HJ, Liang YK, McLachlan DH, Casson S, Isner JC, Wilson I, Neill SJ, Hedrich R, Gray JE, Hetherington AM (2015) Elevated CO2-Induced Responses in Stomata Require ABA and ABA Signaling Curr Biol. pii: S0960-9822(15)01092-1.

This broad collaboration between UK, German and Chinese researchers is led by Alistair Hetherington (Bristol) and Julie Gray (Sheffield) and looks into the molecular events that respond to changing levels of CO2, specifically in guard cells. The new findings in this manuscript show that reduction in stomatal density in response to higher [CO2] relies on the production of reactive oxygen species (ROS), adding a new element to this signaling pathway. In addition they show that the ABA response pathway is also involved in this process and that, following genetic analysis, the CO2 response is mediated via this hormone pathway. However it is unclear whether this is due to ABA increasing CO2 sensitivity in this system or whether CO2 acts specifically in guard cells to increase ABA biosynthesis. A plants response to CO2 is ancestral in evolutionary terms so the authors suggest that this link with ABA signaling is similarly ancient.


Zhai J, Bischof S, Wang H, Feng S, Lee TF, Teng C, Chen X, Park SY, Liu L, Gallego-Bartolome J, Liu W, Henderson IR, Meyers BC, Ausin I, Jacobsen SE (2015) A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis. Cell. 163(2):445-55

GARNet Advisory Board member Ian Henderson is an author in this rare plant-focused paper in Cell, in work that results from his post-doc with Steve Jacobson at UCLA. The manuscript describes a novel mode of action surrounding the plant-specific RNA Polymerase IV (Pol IV). RNAs generated from the activity of Pol IV play an important role in RNA-directed DNA methylation. Intriguingly the authors found that Pol IV transcripts are surprisingly short, just 30 to 40 nt and are similarly adundant to the siRNAs that they subsequently form. The Pol IV RNAs exhibit transcriptional start points similar to those generated by Pol II, which might indicate there are similar mechanisms that control their activity. In addition they find that methylated DNA plays a role in locally reinforcing the silencing reaction. Overall this indicates that the transcripts produced by Pol IV go through a unique “one precursor, one siRNA” model, although the physiological significance of this remains opaque. Another paper on this topic is presented in ELife by the lab of Craig Pikaard.


Provart et al (2015) 50 years of Arabidopsis research: highlights and future directions New Phytol.

Also worth noting this week is a Tansley Review in New Phytologist, which coincides with 50 years since the inaugural Arabidopsis Conference held in 1965. This review has been written by a number of senior Arabidopsis researchers, although no-one from the UK, to discuss the many important findings that have resulted from work on our favourite organism.

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Welcome , today is Wednesday, April 26, 2017