Arabidopsis Research Roundup: May 17th

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Published on: May 17, 2017

This weeks Arabidopsis research roundup begins with a paper led by CPIB at the University of Nottingham that discovers a somewhat surprisingly mechanism controling Arabidopsis root hydrotropism. Next are two papers from the University of Leeds that firstly investigate how the JAGGED LATERAL ORGANS gene influences the auxin response and secondly looks at the role of redox regulation in the control of the cell cycle and seed development. Finally are two papers that look at different aspects of the plant pathogen interactions. Jonathan Jones from the John Innes Centre is a co-author on a paper that dissects the multiple gene expression networks that control plant immunity whilst Charles Melnyk at the Sainsbury lab in Cambridge is involved with work that investigates the hormonal control mechanisms that influence the invasion of parasitic plants.


Dietrich D, Pang L, Kobayashi A, Fozard JA, Boudolf V, Bhosale R, Antoni R, Nguyen T, Hiratsuka S, Fujii N, Miyazawa Y, Bae TW, Wells DM,, Owen MR,, Band LR,, Dyson RJ, Jensen OE, King JR, Tracy SR, Sturrock CJ,, Mooney SJ, Roberts JA, Bhalerao RP, Dinneny JR, Rodriguez PL, Nagatani A, Hosokawa Y, Baskin TI, Pridmore TP, De Veylder L, Takahashi H, Bennett MJ (2017) Root hydrotropism is controlled via a cortex-specific growth mechanism. Nature Plants

http:/​/​dx.​doi.​org/10.1038/nplants.2017.57

Open Access via access link: http://rdcu.be/rSsk

Malcolm Bennett (University of Nottingham) leads a broad international collaboration that looks at the response of Arabidopsis roots to water. Surprisingly they show that this response occurs not in the root meristem but in the elongation zone and is controlled by a ABA signaling mechanism. They show that hydrotropism is dependent on cell elongation in the cortex but not in any other cell file. This is different to the gravitropic response and demonstrates that these tropisms are controlled by distinct tissue-specific mechanisms. To provide for information about this paper, lead author Daniela Dietrich joins Professor Bennett to discuss this paper on the GARNet YouTube channel and speculate on the function of different root cell layers in water uptake.


Rast-Somssich MI, Žádníková P, Schmid S, Kieffer M, Kepinski S, Simon R (2017) The Arabidopsis JAGGED LATERAL ORGANS (JLO) gene sensitizes plants to auxin. J Exp Bot.

http:/​/​dx.​doi.​org/10.1093/jxb/erx131 Open Access

This German-led study includes Stefan Kepinski (University of Leeds) as a co-author. They investigate the role of the JAGGED LATERAL ORGANS (JLO) transcription factor in the establishment of the stem cell niche in the root meristem. JLO interacts with auxin signaling pathway by influencing the degradation of the key regulator BODENLOS (BDL) via the TIR1-mediated degradation pathway. In jlo mutants BDL remains present in the meristem, which does not correctly develop. They discover a novel regulatory mechanism wherein the dosage of the TIR1 and AFB1 auxin receptors is reduced, which in turn prevents BDL degradation. This shows that the JLO transcription factor is a key upstream regulator of meristem formation by playing a significant role in the fine control of the auxin response.


De Simone A, Hubbard R, Vinegra de la Torre N, Velappan Y, Wilson M, Considine MJ, Soppe W, Foyer CH (2017) Redox changes during the cell cycle in the embryonic root meristem of Arabidopsis thaliana. Antioxid Redox Signal. http:/​/​dx.​doi.​org/10.1089/ars.2016.6959

Open Access

Christine Foyer (University of Leeds) collaborates with Australian and German researchers to unpick the role that redox regulation plays in the control of the plant cell cycle. They use an in vivo redox reporter (roGFP2) to show that a cycle of reduction and oxidation occurs throughout the cell cycle. Their experimental system is Arabidopsis seed germination and they show that vitamin c defective mutants with low redox buffering capacity have altered germination rates that coincide with a changed dry seed transcriptome. Overall this paper demonstrates that the cell cycle and embryo size are linked to redox regulation.


Hillmer RA, Tsuda K, Rallapalli G, Asai S, Truman W, Papke MD, Sakakibara H, Jones JDG, Myers CL, Katagiri F (2017) The highly buffered Arabidopsis immune signaling network conceals the functions of its components. PLoS Genet. http:/​/​dx.​doi.​org/10.1371/journal.pgen.1006639

Open Access

Jonathan Jones (John Innes Centre) is a co-author on this Japanese-led research that studies the signaling networks invovled in plant immunity. They use a systems biology approach to dissect the network of interactions that occur within the transcriptome when plants are exposed to the immune stimulant flagellin-22. This analysis discovers that there are separated networks that represent pathways controlled by different higher-level signals, such as jasmonate or salicylic acid. This provides the entire network with a degree of buffering that allows a more effective response to pathogen attack. This type of network analysis is able to reveal facets of the defence response that would not be possible when using simple null mutant analysis so adds consideration detail to the already complicated story of plant-pathogen interactions


Spallek T, Melnyk CW, Wakatake T, Zhang J, Sakamoto Y, Kiba T, Yoshida S, Matsunaga S, Sakakibara H, Shirasu K (2017) Interspecies hormonal control of host root morphology by parasitic plants. PNAS

http:/​/​dx.​doi.​org/10.1073/pnas.1619078114

Charles Melnyk (Sainsbury Lab, Cambridge) is an author on this study led by Ken Shirasu at RIKEN and uses Arabidopsis to investigate the relationship between parasitic plants and their hosts, specifically at the level of interspecies transport via a structure called the haustorium. Haustoria are structures through which substances, such as RNA and proteins, reciprocally move between host and parasite. In this paper they look at the interaction between Arabidopsis roots and the hemiparasitic plant Phtheirospermum japonicum, demonstrating that movement of molecules between species occurs via haustoria once a vascular connection is made. Arabidopsis secondary root growth is induced under infection, a response that requires the effect of the hormone cytokinin. They look at the genetics of this interaction and show that cytokinin signaling genes are important in establishing root hypertrophy. Overall this study demonstrates the important of cytokinin during infection with parasitic plants and might be an important target to design strategies to combat these negative interactions in systems.

Arabdopsis Research Roundup: May 11th

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Published on: May 11, 2017

This weeks Arabidopsis Research Roundup is lead by two papers that characterise the relationship between cell size and growth in different Arabidopsis tissues. Firstly the lab of GARNet PI Jim Murray look at how the cell cycle influences cell size progression in the SAM whilst George Bassel’s group from Birmingham investigate cell growth within a developing embryo. Thirdly is a paper from the University of Essex that further defines the role of the CP12 protein in control of photosynthesis. Next is a paper from researchers from the University of Warwick who lead a fascinating piece of rocket science that identifies differences in the vernalisation requirement across Brassica species whilst in the fifth paper, researchers from Lancaster identify environmentally defined QTLs that determine the plant response to glutamate. Finally is a paper that highlights a new software tool that has the self-explanatory title of the ‘UEA small RNA Workbench’ and is applicable for use with plant-derived datasets.

R Jones A, Forero-Vargas M, Withers SP, Smith RS, Traas J, Dewitte W, Murray JAH (2017) Cell-size dependent progression of the cell cycle creates homeostasis and flexibility of plant cell size. Nat Commun http:/​/​dx.​doi.​org/10.1038/ncomms15060

Open Access

This study comes from the lab of current GARNet PI Jim Murray at the Cardiff University. Lead author Angharad Jones kindly provides an audio description of the paper for the GARNet YouTube channel. This  investigation looks at the factors that control the interaction between cell size and cell growth in a developing shoot meristem. They show that the dynamic regulation of this relationship is linked to the activity of two cyclin dependent kinases (CDKs) and that cell size is key in controlling the transition from G1>S and from G2>M phases of the cell cycle. Importantly this work uses precise imaging to track the progression of individual cell lineages and is therefore able to suggest that cell size is an emergent and not a directly determined property.


Souza NM, Topham AT, Bassel GW (2017) Quantitative analysis of the 3D cell shape changes driving soybean germination. J Exp Bot. http:/​/​dx.​doi.​org/10.1093/jxb/erx048

Open Access

George Bassel (University of Birmingham) leads this paper that uses information gained from the study of patterns of cell expansion in Arabidopsis embryos to investigate a similar process in soybean. Indeed as in Arabidopsis they show that there is preferential early cell expansion closest to the soybean radicle and that starting cell size corresponds to different growth rates. In addition they show that the growing hypocotyl has complex regulation and that differential ansiotrophy growth drives forward the process of germination. Ultimately they show that this occurs equivalently in both model and crop species.


Elena López-Calcagno P, Omar Abuzaid A, Lawson T, Anne Raines C (2017) Arabidopsis CP12 mutants have reduced levels of phosphoribulokinase and impaired function of the Calvin-Benson cycle. J Exp Bot http:/​/​dx.​doi.​org/10.1093/jxb/erx084 Open Access
This study from the photosynthesis group at the University of Essex is led by Tracey Lawson and GARNet committee member Christine Raines. They investigate the role of the CP12 multigene family that has three members in Arabidopsis. These are redox-sensitive proteins that facilitate the formation of a complex between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) during the Calvin-Benson cycle. They show that plants with reduced levels of CP12-1 or CP12-2 have lower photosynthetic capacity and subsequently exhibit slower growth. The cell biological explanation for this alteration appears to focus on the PRK protein, which is present at lower levels in plants with reduced CP12-1 or CP12-2. Therefore the authors find that CP12-1 and CP12-2 are the key members of this gene family and they likely show functional redundancy in the tight control of photosynthesis.


Taylor JL, Massiah A, Kennedy S, Hong Y, Jackson SD (2017) FLC expression is down-regulated by cold treatment in Diplotaxis tenuifolia (wild rocket), but flowering time is unaffected. J Plant Physiol.

http:/​/​dx.​doi.​org/10.1016/j.jplph.2017.03.015 Open Access
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Steve Jackson (University of Warwick) leads this work that also features Chinese collaborators and investigates the role of FLOWERING LOCUS C (FLC) in the popular peppery salad plant Rocket (Diplotaxis tenuifolia) that, as a Brassica, is a somewhat closely related to Arabdopsis. The authors studied the vernalisation requirement in this plant so isolated its version of FLC, which was shown to functional compliment an Arabidopsis flc null mutant. However they showed that even though cold treatment reduced levels of DtFLC this did not alter the bolting time of the plant. This somewhat surprising result demonstrates that the link between FLC and flowering time is uncoupled in this species and that other mechanisms may take precedence, a situation different to that observed in Arabidopsis and other Brassicas.


Walch-Liu P, Meyer RC, Altmann T, Forde BG (2017) QTL analysis of the developmental response to L-glutamate in Arabidopsis roots and its genotype-by-environment interactions. J Exp Bot.

http:/​/​dx.​doi.​org/10.1093/jxb/erx132 Open Access Researchers from the groups of Brian Forde (Lancaster University) and Thomas Altmann (Leibniz Institute) collaborate in this research that identifies three novel QTLs (GluS1-3) that are involved in the response of Arabdopsis roots to external L-glutamate. When this experiment was extended they discovered that different environmental factors play a significant role in the control of this trait. The GluS1 locus is located on Chr3 yet is epistatically controlled by loci on Chr1 and Chr5 in response to temperatures. Overall this study demonstrates that the response to glutamate is controlled by multiple environmentally sensitive loci that vary between Arabidopsis ecotypes


Mohorianu I, Stocks MB, Applegate CS, Folkes L, Moulton V (2017) The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis. Methods Mol Biol.

http:/​/​dx.​doi.​org/10.1007/978-1-4939-6866-4_14

This manuscript from the University of East Anglia describes a set of software tools for the analysis of small RNAs. They used an Arabidopsis dataset to demonstrate the utility of the UEA small RNA Workbench, which can be found here: http://srna-workbench.cmp.uea.ac.uk/

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: http://www.snakesandspiders.com/wp-content/uploads/2013/05/red-spider-mite-control.jpg

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

http:/​/​dx.​doi.​org/10.1016/j.cub.2017.01.030

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.

http:/​/​dx.​doi.​org/10.1093/jxb/erx015

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: March 17th

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Published on: March 17, 2017

This weeks UK Arabidopsis Research Roundup includes three papers featuring researchers from the University of Nottingham as well as manuscripts from Leeds, Lancaster, QMUL and The Sainsburys Lab in Norwich

Firstly Stefan Kepinski (Leeds) leads a study that investigates how Gravitropic Set Point Angle (GSA) is controlled in response to different growth factors. Secondly are two Methods papers featuring researchers from CPIB in Nottingham, the first of which is in collaboration with Lancaster University and introduces the Microphentron, which is an automated phenotyping platform that can be used for chemical biology screens. The second paper describes a non-destructive method for imaging floral tissues using CT scanning.

Ranjan Swarup is also a member of CPIB and in the next paper he has collaborated with French colleagues to investigate the role of SHR on root development in rice.

The fourth paper includes Cyril Zipfel as a co-author and investigates the role of damage-associated molecular patterns (DAMPs) in the response to pathogen attack whereas this weeks final paper is from the lab of Alexander Ruban (QMUL) and discovers the phenotypic consequences of persistent damage to PSII by photoinhibition.


Suruchi Roychoudhry, Martin Kieffer, Marta Del Bianco, Che-Yang Liao, Dolf Weijers Stefan Kepinski (2017) The developmental and environmental regulation of gravitropic setpoint angle in Arabidopsis and bean Scientific Reports http://dx.doi.org/10.1038/srep42664

Open Access

Stefan Kepinski (University of Leeds) leads this study that involves a collaboration with Dolf Weijers from Wageningen University. They investigate the role of both auxin and environmental factors in determining gravitropic set point angle (GSA), which is a measure of the growth of lateral organs away from primary shoots and roots. They show that nitrogen and phosphorous deficiency causes opposing effects on lateral root GSA, each of which are auxin-dependent. This contrasts with previous findings from work using bean adventitious roots. They find that these differences are maintained when Arabidopsis and bean roots are treated with different auxin concentrations. Latterly they also look at the effect of different light conditions on shoot GSA and put these findings into the context of potentially altering crop growth.

Stefan takes some time to discuss this paper for the GARNet YouTube Channel.


Burrell T, Fozard S, Holroyd GH, French AP, Pound MP, Bigley CJ, James Taylor C, Forde BG (2017) The Microphenotron: a robotic miniaturized plant phenotyping platform with diverse applications in chemical biology. Plant Methods

http://dx.doi.org/10.1186/s13007-017-0158-6 Open Access

This methods paper is a collaboration between the Universities of Lancaster and Nottingham led by Brian Forde that describes the Microphenotron. This device has been developed to facilitate chemical biology screens on in vivo plant tissues. This allows for the automated screening of either dicot or monocot roots or aerial tissues that have been grown on media infused with whichever chemical is relevant for the intended expriments. In situ GUS screening is also possible allowing for researchers to integrate information about growth and gene expression. The use of ‘Phytostrips’ in a 96-well format allows for high-throughput screening that is aligned with AutoRoot automated image analysis software to provide a rapid and facile method for undertaking small scale phenotypic screens. The Microphenotron facility is housed at the Lancester University, who are extremely open to collaboration so please get in contact if you are interested in using the facility.


Tracy SR, Gómez JF, Sturrock CJ, Wilson ZA, Ferguson AC (2017) Non-destructive determination of floral staging in cereals using X-ray micro computed tomography (µCT) Plant Methods. http://dx.doi.org/10.1186/s13007-017-0162-x Open Access

Alison Ferguson is the corresponding author on this methods paper that includes GARNet committee member Zoe Wilson and Saoirse Tracy from Dublin. They have developed a technique using X-ray µCT scanning to image developing flowers in Arabidopsis and barley plants, taking advantage of the excellent Hounsfield facility at the University of Nottingham. They show that the technique can be hugely beneficial for plant phenotyping by providing a non-destructive method of analyzing live floral development and how this can response to changes in the growth environment. Members of the Hounsfield facility are happy to discuss any potential collaborative work and future access to these type of facilities will hopefully be improved through the UKs involvement in the pan-european EMPHASIS project.


Henry S, Dievart A, Fanchon D, Pauluzzi G, Meynard D, Swarup R, Wu S, Lee CM, Gallagher K, Périn C (2017) SHR overexpression induces the formation of supernumerary cell layers with cortex cell identity in rice. Dev Biol. http://dx.doi.org/10.1016/j.ydbio.2017.03.001

Ranjan Swarup (CPIB) is a co-author on this study that includes French and US researchers. Previously they had shown that expression of rice SHORTROOT (OsSHR) genes could compliment the Arabidopsis shr mutant. In this study they show that overexpression of OsSHR and AtSHR in rice roots causes growth of wider, shorter roots that have an increased number of cortical cell layers. This demonstrates that the mechanisms that control the differentiation of cortical cell layers is conserved throughout land plants, with SHR being a key determinant in this process.


de Azevedo Souza C, Li S, Lin AZ, Boutrot F, Grossmann G, Zipfel C, Somerville S (2017) Cellulose-derived oligomers act as damage-associated molecular patterns and trigger defense-like responses. Plant Physiol. http://dx.doi.org/10.1104/pp.16.01680

Cyril Zipfel (The Sainsbury Lab) is a co-author on this study from the lab of Shauna Somerville in California that focuses on the concept of damage-associated molecular patterns (DAMPs). These can be defined as cell wall breakdown components and stimulate the same defence responses as more fully characterised pathogen- or microbe-associated molecular patterns (PAMPs). Intuitively this makes sense as during infection many pathogens will cause cell wall breakdown. The authors show that cellulose-derived oligomers trigger a signalling response similar to that caused by oligogalacturonides or chito-oligomers but that lacks an increase in ROS or in callose deposition. These results confirm that cellulose-derived signals feed into the plants mechanism for cell wall scanning and acts synergistically with other signals that result from pathogen attack.


Tian Y, Ungerer P, Zhang H, Ruban AV (2017) Direct impact of the sustained decline in the photosystem II efficiency upon plant productivity at different developmental stages. J Plant Physiol. http://dx.doi.org/110.1016/j.jplph.2016.10.017

Image from http://www.sciencedirect.com/science/article/pii/S0176161717300433

Alexander Ruban (QMUL) leads this Sino-UK collaboration that investigates how the photoinhibiton of photosystem II impacts overall plant growth. In this study they use lincomycin to block chloroplast protein synthesis, which prevents the plant from restoring PSII function after photoinhibitory damage. Treated plants accumulate less starch and showed reduced above-ground biomass. This leads to a decrease in seed yield. Perhaps unsurprisingly this research shows that restoring the full function of PSII after photoinhibition to key to maintaining normally functioning electron transport rate that leads into metabolic production and growth rate.

Arabidopsis Research Roundup: March 6th.

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Published on: March 6, 2017

This weeks Arabidopsis Research Roundup includes four papers that focus on different aspects of plant cell biology. Firstly Ian Henderson’s research group in Cambridge defines the role of a critical component that determines crossover frequency in plants and other eukaryotes. Secondly Karl Oparka (Edinburgh) leads a broad collaboration that defines the mechanism of unloading of solutes and macromolecules from the root phloem. Thirdly Keith Lindsey (Durham) has developed a model that describes how auxin patterns the Arabidopsis root. Finally Mike Blatt (Glasgow) is part of a group that uses Arabidopsis as a framework for the study of ABA-signaling during stomatal movement in ferns.


Ziolkowski PA, Underwood CJ, Lambing C, Martinez-Garcia M, Lawrence EJ, Ziolkowska L, Griffin C, Choi K, Franklin FC, Martienssen RA, Henderson IR (2017) Natural variation and dosage of the HEI10 meiotic E3 ligase control Arabidopsis crossover recombination. Genes Dev

http:/​/​dx.​doi.​org/10.1101/gad.295501.116

Open Access

GARNet committee member Ian Henderson (University of Cambridge) leads this work that features collaborators from the UK, US and Poland. They use an experimental technique that allows facile analysis of recombination rates alongside a study of Arabidopsis natural variation to isolate a QTL that is critical for maintaining the correct number of crossovers during meiosis. This HEI10 gene codes for an E3 ligase (the targets of which are currently unknown) whose copy number is a key component in the control of recombination rate. Hei10 mutants have less crossovers whilst plants with extra copies of HEI10 have an increased number, especially in sub-telomeric regions of the genome. HEI10 is a highly conserved protein, demonstrating its important role to ensure appropriate levels of recombination throughout the evolution of eukaryotes.

Ian kindly takes ten minutes to discuss this paper with GARNet on our YouTube Channel.


Ross-Elliott TJ, Jensen KH, Haaning KS, Wager BM, Knoblauch J, Howell AH, Mullendore DL, Monteith AG, Paultre D, Yan D, Otero-Perez S, Bourdon M, Sager R, Lee JY, Helariutta Y, Knoblauch M, Oparka KJ (2017) Phloem unloading in Arabidopsis roots is convective and regulated by the phloem-pole pericycle. Elife.

http:/​/​dx.​doi.​org/10.7554/eLife.24125

Open Access

Karl Oparka (University of Edinburgh) is the corresponding author of this study that includes researchers from the UK, US and Denmark. Movement of solutes and macromolecules through the plant phloem is key for the correct distribution of nutrients allowing for optimal growth. In this paper they discover that unloading of molecules from the phloem occurs via a set of specialized funnel plasmodesmata that link the phloem to adjacent pericycle cells. Remarkably they find that whereas solutes are constantly unloaded, larger proteins are released through these plasmodesmata in discrete pulses, which they describe as ‘batch unloading’. Overall this study provides evidence of a major role for the phloem-pericycle cells in the process of moving essential nutrients from the phloem into surrounding tissues.


Moore S, Liu J, Zhang X, Lindsey K (2017) A recovery principle provides insight into auxin pattern control in the Arabidopsis root. Sci Rep. http:/​/​dx.​doi.​org/10.1038/srep43004

Open Access

The work comes from the lab of Keith Lindsey (University of Durham) and developes a data-driven model that predicts the role of auxin patterning in the recovery of an Arabidopsis root following a perturbation of polar auxin transport. They demonstrate three main principles that define the role of auxin influx and efflux carriers in this process and also provide experimental validation for their predictions.


Cai S, Chen G, Wang Y, Huang Y, Marchant B, Wang Y, Yang Q, Dai F, Hills A, Franks PJ, Nevo E, Soltis D, Soltis P, Sessa E, Wolf PG, Xue D, Zhang G, Pogson BJ, Blatt MR, Chen ZH (2017)

Evolutionary Conservation of ABA Signaling for Stomatal Closure in Ferns Plant Physiol

http:/​/​dx.​doi.​org/10.1104/pp.16.01848

Open Access

Mike Blatt (University of Glasgow) is a co-author on this global study that looks into the evolution of ABA-signaling in the control of stomatal closure. Although this study is focused on this process in ferns they build their findings on the analysis of transcriptional networks from Arabidopsis. Ultimately they find that the evolution of ABA-controlled guard cells movements are important in the adaptation of ferns to a terrestrial environment.

Arabidopsis Research Roundup: February 27th

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Published on: February 28, 2017

This weeks research roundup includes just three papers and includes a study from the University of Essex that looks at the growth response of Arabidopsis plants to ‘real-life’ fluctuations in light levels. Secondly is a very different type of study from the University of York that uses Arabidopsis as a model for the development of plants that are able to accumulate catalytically active and commercially viable levels of palladium. Finally is a Chinese-led study that includes Alan Marchant (University of Southampton) as a co-author and looks at the role of the ERF74-RbohD-ROS signaling module on the response to abiotics stress.

Vialet-Chabrand SR, Matthews JS, Simkin A, Raines CA, Lawson T (2017) Importance of fluctuations in light on plant photosynthetic acclimation Plant Physiol.

http://dx.doi.org/10.1104/pp.16.01767

Open Access

Tracy Lawson and GARNet committee member Christine Raines from the University of Essex Photosynthesis Group lead this study that aims to understand how plants respond to variation in light levels that occur over an ‘average’ day. This contrasts with the conditions used in a ‘standard’ growth chamber and they show that plant growth is significantly altered when the light levels fluctuate, even though the total amount of light that the plant receives is the same. The ultimate conclusion of the study is that the growth of plants under ‘square wave growth conditions’ does not accurately reflect what might be observed in the field. This is significant given the importance of moving research from model organisms, usually grown under controlled conditions into crop species grown in the field.

Tracy Lawson kindly takes less than ten minutes to discuss the paper with GARNet on our YouTube channel.


Harumain ZA, Parker HL, Muñoz García A, Austin MJ, McElroy CR, Hunt AJ, Clark JH, Meech JA, Anderson CW, Ciacci L, Graedel TE, Bruce NC, Rylott EL (2017) Towards financially viable phytoextraction and production of plant-based palladium catalysts. Environ Sci Technol. http://dx.doi.org/ 10.1021/acs.est.6b04821

Open Access

Elizabeth Rylott and Neil Bruce at the University of York lead this study that includes collaborators from the USA, Canada, Malaysia and New Zealand. They look into the options for phytoextraction of palladium, which forms nanoparticles in Arabidopsis roots. The metal taken from these roots had normal catalytic activity and could be obtained at up to 18g/kg dried tissue weight. These experiments were moved into mustard, miscanthus and sixteen willow species and although palladium can be taken up into the plant tissues, it could not be extracted at a level that would make it commercially viable. However the authors are confident that this is am important step toward attempts to develop field-suitable plants that can reduce the environmental impacts of palladium mining.


Yao Y,, He RJ, Xie QL,, Zhao XH,, Deng XM,, He JB,, Song L, He J, Marchant A, Chen XY,, Wu AM (2016) ETHYLENE RESPONSE FACTOR 74 (ERF74) plays an essential role in controlling a respiratory burst oxidase homolog D (RbohD)-dependent mechanism in response to different stresses in Arabidopsis. New Phytol. 213(4):1667-1681. http://dx.doi.org/10.1111/nph.14278

Alan Marchant (University of Southampton) is a co-author on this Chinese-led study that focuses on the role of the ERF74 transcription factor from the ETHYLENE RESPONSE FACTOR VII (ERF-VII) family in the response to abiotic stresses. The authors test the responses of plants with changed levels of ERF74, showing that they have altered responses to a range of stresses such as drought, light, heat and aluminum. erf74 mutants lack a typical reactive oxidative stress (ROS) burst due to low expression of the RESPIRATORY BURST OXIDASE HOMOLOG D (RbohD) protein. ERF74 directly interacts with the RbohD promotor and the paper shows that the whole ERF74-RbohD-ROS signaling module is activated in order for the plant to correctly response to a range of stresses, which each require maintenance of hydrogen peroxide homeostasis.

Arabidopsis Research Roundup: February 20th

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Published on: February 19, 2017

This weeks Arabidopsis Research Roundup begins with two papers that look at endogenous and exogenous causes of cell proliferation. Firstly Mike Bevan (JIC) leads a team that looks into the role of controlled protein degradation in this process whilst secondly, Peter Etchells from Durham is a co-author on a study that investigates how nematode pathogens stimulate cell proliferation at the site of infection.

Thirdly is work featuring Cyril Zipfel and colleagues from TSL that looks at how autophosphorylation controls the activity of calcium dependent protein kinases. Fourthly is a broad collaboration led by Richard Mott (UCL) that uses genomic structural variation to identify novel loci. Next Simon Turner from the University of Manchester phylogenetically defines the RALK peptide lineages across plant species. Finally researchers at the University of York conduct a structural analysis of the Arabidopsis AtGSTF2 glutathione transferase.


Dong H, Dumenil J, Lu FH, Na L, Vanhaeren H, Naumann C, Klecker M, Prior R, Smith C, McKenzie N, Saalbach G, Chen L, Xia T, Gonzalez N, Seguela M, Inze D, Dissmeyer N, Li Y, Bevan MW (2017) Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis.

Genes Dev. http:/​/​dx.​doi.​org/10.1101/gad.292235.116

Open Access


Mike Bevan (John Innes Centre) is the corresponding author of this study that also includes researchers from labs in Belgium, Germany and China. They investigate a fundamental determinant of organ shape, the pattern of cell proliferation that leads to final cell size. They show that two RING E3 ligases activate the DA1 peptidase that in turn affects the stabilization and activity of a range of other proteins including the transcription factors TEOSINTE BRANCED 1/CYCLOIDEA/PCF 15 (TCP15) and TCP22. Overall this results in continued cell proliferation and repression of endoreduplication, which ultimately serves to regulate the timing of the transition from cell proliferation to organ differentiation.

Mike discusses the science surrounding this paper on the GARNet YouTube channel.


Guo X,, Wang J, Gardner M, Fukuda H, Kondo Y, Etchells JP, Wang X, Mitchum MG. Identification of cyst nematode B-type CLE peptides and modulation of the vascular stem cell pathway for feeding cell formation. PLoS Pathog. http:/​/​dx.​doi.​org/10.1371/journal.ppat.1006142

Open Access

Peter Etchells (University of Durham) is a co-author on this US-led study that looks at the effect of nematode-delivered CLE-like peptides on cell growth and how that impacts parasitism. This study has identified a new class of peptides from nematodes that are similar to the plant B-type CLE-like peptide TDIF (tracheary element differentiation inhibitory factor). They show that the nematodes alter the activity of the TDIF-TDR (TDIF receptor)-WOX4 signaling module during infection, whose endogenous function acts during procambial meristem cell proliferation. A variety of mutants involved in this process show reduced infection and leading to the hypothesis that WOX4 is a potential target for nematode CLEs. When exogenous nematode CLE peptides are added to Arabidopsis roots they cause massive cell proliferation. This demonstrates that this response is clearly important for the establishment of nematode infection, usually in cambial cell files.


Bender KW, Blackburn RK, Monaghan J, Derbyshire P, Menke FL, Zipfel C, Goshe MB, Zielinski RE, Huber SC (2017) Autophosphorylation-based calcium (Ca2+) sensitivity priming and Ca2+/Calmodulin inhibition of Arabidopsis thaliana Ca2+-dependent protein kinase 28 (CPK28) J Biol Chem.

http:/​/​dx.​doi.​org/10.1074/jbc.M116.763243

Cyril Zipfel (The Sainsbury Lab) features for a second consecutive week on the Arabidopsis research roundup, this time as a co-author in a study that investigates the role of autophosphorylation in the regulation of calcium (Ca2+) dependent protein kinases (CPKs). In addition they evaluated the role of Calmodulin (CaM) on the activity of CPKs, something that had been previously overlooked. Indeed they show that CPK28 is a CaM-binding protein and that autophosphorylation causes increased activity, especially in low Ca2+ concentrations. Therefore this research provides a mechanistic insight into how a cell might respond to low levels of Ca2+.


Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits. Genetics. http:/​/​dx.​doi.​org/10.1534/genetics.116.192823

Open Access

Richard Mott (UCL) is corresponding author on this paper includes authors from throughout the UK, Europe and the US. They provide a new analysis of Arabidopsis populations that relies on the genome structural variation. They treat these structural variants as quantitative traits and subsequently map genetically in the same way as in a gene expression study. When a structural variant locus is linked to a genotype at a distant locus then it is designated as a site of transposition. Remarkably they show 25% of the structural variants can be assigned to the transposition events. This method of assessing structural variant loci is amendable to sequencing at low-coverage and this study identified loci that might be involved in germination and resistant to pathogens. Overall they find that genes within structural variants are more likely to be silenced and that this novel analysis technique is particularly useful when mapping transposition events.


Campbell L, Turner SR1(2017) A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups. Front Plant Sci. http:/​/​dx.​doi.​org/10.3389/fpls.2017.00037

Open Access

This study from the lab of Simon Turner (University of Manchester) analyse Rapid Alkalinization Factor (RALFs) cysteine-rich peptides from across 51 plant species. They infer that these plant RALFs originate from four major clades in which the majority of the variation exists in the mature peptide sequence, indicative of clade-specific activities. Clade IV accounts for a third of the total peptides yet these lack a number of sequence features thought to be important for RALF function, which leads the authors to speculate that this clade should be thought of as containing RALF-related peptides instead of regular RALFs. Further experimental work is needed in order to define the true nature of the functional relationship between Clades I-III and Clade IV.


Ahmad L, Rylott EL, Bruce NC, Edwards R, Grogan G (2016) Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands. FEBS Open Bio. http:/​/​dx.​doi.​org/10.1002/2211-5463.12168

Open Access

This paper links plant science and structural biology in a study that was undertaken at the University of York. Plant Glutathione transferases (GSTs) have multiple roles including in the detoxification of xenobiotics as well as in various non-catalytic roles. In this work the structure of the Arabidopsis AtGSTF2 is revealed in tandem with a variety of non-catalytic partners including indole-3-aldehyde, camalexin, the flavonoid quercetrin and its non-rhamnosylated analogue quercetin. These are thought to bind to AtGSTF2 by hydrophobic interactions at either one or two symmetrical binding sites. The authors speculate that this non-catalytic binding might have a possible role in ligand transport.

Arabidopsis Research Roundup: Feb 9th

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Published on: February 14, 2017

This weeks Arabidopsis Roundup again includes a broad selection of research topics. Firstly researchers at SLCU are involved in work that describes Arabidopsis sepal development. Secondly Cyril Zipfel from TSL leads a study that adds a layer of complexity to our knowledge of cellular pathogen perception. Thirdly the group of Reiner van der Hoorn from Oxford introduces the use of a novel set of inhibitors that reveals differential activity of proteosomal subunits during bacterial infection. Finally Hugh Pritchard from Kew Gardens is a co-author on a lipidomic study of the seed dessication-stress response.

Meyer HM, Teles J, Formosa-Jordan P, Refahi Y, San-Bento R, Ingram G, Jönsson H, Locke JC, Roeder AH (2017) Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. Elife.

http:/​/​dx.​doi.​org/10.7554/eLife.19131

Open Access

James Locke and Henrik Jonsson (SLCU) are authors on this paper that is led by Adrienne Roeder at Cornell in the USA. The Roeder lab largely focused their research on development of the sepal. The SLCU researchers provided modeling support for this investigation into the critical role of the ATML1 gene in the differentiation of initially identical cells into giant or regular sized sepal cells. They show that there it is a threshold level of differential ATML1 expression that is key in determining cell fate. If this threshold is met during the G2 phase of the cell cycle the cells enter endoreduplication and become giant. If the threshold isn’t reached then the cells divide and remain at a ‘normal’ size. Ultimately they demonstrate a fluctuation-driven patterning mechanism that determines cell fate.

Stegmann M, Monaghan J, Smakowska-Luzan E, Rovenich H, Lehner A, Holton N, Belkhadir Y, Zipfel C (2017) The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling Science

http:/​/​dx.​doi.​org/10.1126/science.aal2541

Cyril Zipfel (The Sainsbury Lab, Norwich) is the lead author of this study that builds upon his labs work into mechanisms of pathogen perception by cell-surface receptor kinases. In this latest work they show that the SITE-1 PROTEASE (ST1P) cleaves endogenous RAPID ALKALINIZATION FACTOR (RALF) propeptides to inhibit plant immunity, a response mediated via the receptor kinase FERONIA (FER). The FER protein is also involved in the formation of other immune complexes. The authors have discovered a mechanism by which FER reglates RALK signaling, indicating that they might have uncovered a more general mechanism for this key control point of immune signaling.

Misas-Villamil JC,, van der Burgh AM, Grosse-Holz F, Bach-Pages M, Kovács J,, Kaschani F, Schilasky S, Emon AE, Ruben M, Kaiser M, Overkleeft HS, van der Hoorn RA (2017) Subunit-selective proteasome activity profiling uncovers uncoupled proteasome subunit activities during bacterial infections. Plant Journal

http:/​/​dx.​doi.​org/10.1111/tpj.13494

Reiner van der Hoorn (University of Oxford) lead this cross-Europe collaboration that introduces a range of inhibitors and probes that can discriminate between catalytic subunits of the proteasome. These tools were studied in both Arabidopsis and Nicotiana benthamiana and the authors used the plant-microbe interactions to further validate their specificity. They show that proteasomal subunits have separate paralogs that are differentiatially incorperated into the larger complex depending on an interaction with pathogenic bacteria. Aliquots of these probes are available on request from renier.vanderhoorn@plants.ox.ac.uk

The authors encourage their usage so as to increase the chance that they might become commercially available. More information from the Plant Chemetics lab.

Chen H, Yu X, Zhang X, Yang L, Huang X, Zhang J, Pritchard HW, Li W (2017) Phospholipase Dα1-mediated phosphatidic acid change is a key determinant of desiccation-induced viability loss in seeds. Plant Cell Environ.

http:/​/​dx.​doi.​org/10.1111/pce.12925

Hugh Pritchard (Kew Gardens) is a co-author on this Chinese-led study that investigates the role of phosphatidic acid (PA) on seed viability. Higher levels of PA correlated with lower seed viability after a desiccation stress. Using Arabidopsis seeds they showed that the enzyme phospholipase D α1 (PLD α1) localises to the plasma membrane following desiccation, where it produces PA. When PLD α1 was suppressed, seed recovery following desiccation improved. The authors used comparative lipidomics to compare PA levels in eight plant species and from their Arabidopsis work, they propose a new model for the mechanism by which seed desiccation effects germination rates.

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