Arabidopsis Research Roundup: September 6th

This largest ever Arabidopsis Research Roundup (ARR) includes 6 papers from Norwich Research Park (NRP), including three featuring Cyril Zipfel (TSL) as a co-author on papers that investigate different aspects of plant immune signaling. Elsewhere on the NRP site Veronica Grieneisen (JIC) is a co-author on a study that defines the root auxin maximum whilst Dale Sanders and Saskia Hogenhout lead a paper that defines a method for the analysis of calcium signaling. Finally Robert Sablowski’s group at the JIC investigates the role of the DELLA proteins during meristem development.

Elsewhere investigators from Kew Gardens and Bangor University have used nanopore sequencing for the facile characterisation of field populations of Arabidopsis. Similarly Seth Davies (University of York) is part of a collaboration that looks how alterations in the circadian clock might affect plant fitness.

Verena Kriechbaumer (Oxford Brookes) leads a phylogenetic study into the conservation of auxin biosynthesis genes whilst Hilary Rodgers (Cardiff University) is a co-author on a Chinese-led study that looks into role of cadmium on the Arabidopsis cell cycle.

This ARR is full of examples of UK researchers involved in global collaborations. This includes Cambridge researchers involved in a proteomic analysis of microsomes, Justin Goodrich from the University of Edinburgh as part of a US-led study that defines the regulation of the PRC2 complex and Katherine Denby (University of York) as a member of a consortium that has performed a network analysis of jasmonic acid signaling.

Finally are two studies in which the research takes place within a single institution. Malcolm Hawksford (Rothamsted Research) looks at the effect of wheat transcription factors in the response to the heavy metal zinc whilst Emily Larson and Mike Blatt (University of Glasgow) investigate the role of clathrin on plant vesicular transport.


D’Ambrosio JM, Couto D, Fabro G, Scuffi D, Lamattina L, Munnik T, Andersson MX, Alvarez ME, Zipfel C, Laxalt AM (2017) PLC2 Regulates MAMP-Triggered Immunity by Modulating ROS Production in Arabidopsis. Plant Physiol 10.1104/pp.17.00173

This Argentinian-led study includes Cyril Zipfel (TSL) as a co-author on this work that uses miRNA-mediated gene silencing to assess the role of the phosphoinositide-specific phospholipase C (PI-PLC) in plant immune signaling.


Imkampe J, Halter T, Huang S, Schulze S, Mazzotta S, Schmidt N, Manstretta R, Postel S, Wierzba M, Yang Y, vanDongen WM, Stahl M, Zipfel C, Goshe MB, Clouse S, de Vries SC, Tax F, Wang X, Kemmerling B (2017) The Arabidopsis Leucine-rich Repeat Receptor Kinase BIR3 Negatively Regulates BAK1 Receptor Complex Formation and Stabilizes BAK1. Plant Cell. 10.1105/tpc.17.00376

Cyril Zipfel (TSL) is a co-author on this global collaboration that further defines the role of the BAK1 receptor in hormone and immune signaling through its interaction with two LRR-RK proteins (BIR2 and BIR3).


Singh V, Perraki A, Kim SY, Shrivastava S, Lee JH, Zhao Y, Schwessinger B, Oh MH, Marshall-Colon A, Zipfel C, Huber SC (2017) Tyrosine-610 in the Receptor Kinase BAK1 Does Not Play a Major Role in Brassinosteroid Signaling or Innate Immunity. Front Plant Sci. 10.3389/fpls.2017.01273

Cyril Zipfel (TSL) is a co-author on this US-led manuscript that again looks into the role of the BRI1-ASSOCIATED KINASE1 (BAK1) on plant immune signaling. Importantly they show that the phosphorylation of tyrosine-610 is actually not necessary for this proteins role in brassinosteroid or immune signaling


Di Mambro R, De Ruvo M,,, Pacifici E, Salvi E, Sozzani R, Benfey PN,, Busch W, Novak O, Ljung K, Di Paola L, Marée AFM, Costantino P, Grieneisen VA, Sabatini S (2017) Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A 10.1073/pnas.1705833114

Veronica Grieneisen (JIC) is a co-corresponding author on this work with Sabrina Sabatini from the University of Rome. They define the auxin minimum, a newly characterised determinat of root patterning that delineates the separation of root division and the differentiation zones. This is defined by the interaction between cytokinin and auxin signaling cascades.

Veronica discusses this paper on the GARNet YouTube channel: https://www.youtube.com/watch?v=gYdL6eddOcA


Vincent TR, Canham J, Toyota M, Avramova M, Mugford ST, Gilroy S, Miller AJ, Hogenhout S, Sanders D (2017) Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor. J Vis Exp. 10.3791/56142

Dale Sanders and GARNet committee member Saskia Hogenhout (JIC) lead this study that describes an imaging technique that allows for the real time assessment of calcium dynamics using a fluorescently tagged sensor.


Serrano-Mislata A, Bencivenga S, Bush M, Schiessl K, Boden S, Sablowski R (2017) DELLA genes restrict inflorescence meristem function independently of plant height. Nature Plants. 10.1038/s41477-017-0003-y

Robert Sablowski (JIC) leads this paper that investigates the role of DELLA proteins in the control of cell cycle regulators and how this impacts meristem size in both barley and Arabidopsis. Read more about it on the John Innes Centre website.


Parker J, Helmstetter AJ, Devey D, Wilkinson T, Papadopulos AST (2017) Field-based species identification of closely-related plants using real-time nanopore sequencing. Sci Rep. 10.1038/s41598-017-08461-5 Open Access

This investigation led by researchers at Kew Gardens and at the Bangor University use Real Time Nanopore Sequencing (RTnS) that allows for rapid species identification in the field and that combining RTnS and laboratory-based high-throughput sequencing leads to a significant improvement in genome assembly.


Rubin MJ, Brock MT, Davis AM, German ZM, Knapp M, Welch SM, Harmer SL, Maloof JN7, Davis SJ, Weinig C (2017) Circadian rhythms vary over the growing season and correlate with fitness components. Mol Ecol. 10.1111/mec.14287 Open Access

Seth Davies (University of York) is a co-author on this US-led work that conducts a study of field-growth Arabidopsis to evaluate the contribution of the circadian clock toward survival and fecundity. They show that variation in clock function correlates with growth performance in a natural environment.


Poulet A, Kriechbaumer V (2017) Bioinformatics Analysis of Phylogeny and Transcription of TAA/YUC Auxin Biosynthetic Genes. Int J Mol Sci. 10.3390/ijms18081791 Open Access

The paper from Oxford Brookes University provides a phylogenetic analysis of TAA/TAR (tryptophan aminotransferase related) and YUCCA proteins that are involved in auxin biosynthesis. In addition they provide tissue and cell-specific information about the function of these proteins and that their function is conserved in lower plant species.


Cui W, Wang H, Song J, Cao X, Rogers HJ, Francis D, Jia C, Sun L, Hou M, Yang Y, Tai P, Liu W (2017) Cell cycle arrest mediated by Cd-induced DNA damage in Arabidopsis root tips. Ecotoxicol Environ Saf. 10.1016/j.ecoenv.2017.07.074 Open Access

Hilary Rodgers (Cardiff University) is a co-author on this Chinese-led study that looks into the effect of cadmium treatment on the regulation of the cell cycle and DNA damage repair. They show that different cadmium concentrations effect different phases of the cell cycle.


Alqurashi M, Thomas L, Gehring C, Marondedze C (2017) A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses. Proteomes. 10.3390/proteomes5030022 Open Access

This international collaboration includes members of the Cambridge Centre for Proteomics and conducts a quantitative analysis of the Arabidopsis microsomal proteome following treatment with hydrogen peroxide or ABA. Perhaps unsurprisingly a high number of proteins characterized as ‘responsing to stress’ were found upregulated following treatment with H2O2 or ABA.


Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS,, Bonasio R, Wagner D (2017) Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nature Genet 10.1038/ng.3937

Justin Goodrich (University of Edinburgh) is a co-author on this US-led study that looks into the role of Polycomb response element (PREs) in directing the placement of the Polycomb repressive complex 2 (PRC2) via their interaction with a newly identified transcription factors. Justin has recently discussed a paper on a similar topic on the GARNet YouTube channel.


Hickman R, van Verk MC, Van Dijken AJH, Pereira Mendes M, Vroegop-Vos IA, Caarls L, Steenbergen M, Van Der Nagel I, Wesselink GJ, Jironkin A, Talbot A, Rhodes J, de Vries M, Schuurink RC, Denby K, Pieterse CMJ, Van Wees SCM (2017) Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network. The Plant Cell 10.1105/tpc.16.00958 Open Access

GARNet committee member Katherine Denby (University of York) is a member of this large consortium of researchers who have performed a network analysis on the dynamics of jasmonic acid signaling


Evens NP, Buchner P, Williams LE, Hawkesford MJ (2017) The role of ZIP transporters and group F bZIP transcription factors in the Zn-deficiency response of wheat (Triticum aestivum) Plant J. 10.1111/tpj.13655 Open Access

Malcolm Hawkesford (Rothamsted Research) leads this study that investigate a set of wheat bZIP transcription factors and ZIP transporters that are involved in the uptake and transport of zinc. As part of this work they use Arabidopsis to test the conserved function of these wheat proteins.


Larson ER, Van Zelm E, Roux C, Marion-Poll A, Blatt MR (2017) Clathrin Heavy Chain subunits coordinate endo- and exocytic traffic and affect stomatal movement. Plant Physiol. 10.1104/pp.17.00970 Open Access

Mike Blatt and Emily Larson (University of Glasgow) are the co-corresponding authors on this study that looks into the role of clathrin heavy chain on vesicular transport in Arabidopsis. They looked at clathrin mutants to show that the protein plays an unsurprisingly important role in both endo- and exocytosis.

Arabidopsis Research Roundup: August 23rd

There is a bumper crop of papers in this weeks UK Arabidopsis Research Roundup! First up is a remarkable piece of work from George Bassel’s (University of Birmingham) lab that defines the network of cellular interactions that occur in the hypocotyl. Second and third are papers from the JIC in which Lars Ostergaard’s group uncovers the extent of the ETTIN signaling network and Caroline Dean‘s and Martin Howard’s labs provide evidence for a two step progression toward stable gene silencing following vernalisation at the FLC locus. Fourthly is a study that includes members of Alex Webb’s group (University of Cambridge) as co-authors that investigates the link between the circadian clock and night time starch metabolism. Fifth is a paper from Christine Foyer (University of Leeds) that looks at the effect of commonly used inhibitors on cellular redox state and gene expression. The next paper includes Phillip Carella (SLCU) as a co-author and looks at the role of classic flowering time genes on the phenomenon of Age-Related Resistance and finally Lee Sweetlove’s (University of Oxford) lab has published a methods paper for the analysis of photorespiration in non-photosynthetic tissues.


Jackson MD, Xu H, Duran-Nebreda S, Stamm P, Bassel GW (2017) Topological analysis of multicellular complexity in the plant hypocotyl. Elife http:/​/​dx.​doi.​org/10.7554/eLife.26023

Open Access

George Bassel (University of Birmingham) is the corresponding author on this work that provides fantastic images of the plant hypocotyl taken as part of an analysis on the cell growth dynamics in this organ. They show that Arabidopsis epidermal atrichoblast cells demonstrate a reduced path length that coincides with preferential movement of small molecules through these cells. They analysis this process in various mutants showing which gene activities were necessary for the construction of this pattern. In addition they compared topological features in Arabidopsis, Poppy and Foxglove, showing that cell interactions and path length determinants differ between these organisms. Overall this manuscript defines the network principles that control complex organ construction as well as a function for higher order patterning.


Simonini S, Bencivenga S, Trick M, Ostergaard L (2017) Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis. Plant Cell 10.1105/tpc.17.00389

Open Access

Last year Lars Ostergaard (JIC) discussed a paper from his lab on the GARNet YouTube channel in which they defined a new auxin-signaling paradigm that involved the non-canoical Auxin Response Factor ETTIN. This follow up to that study investigates the genetic network controlled by ETTIN activity and defines a range of developmental processes dependent on ETTIN auxin sensing. Furthermore by looking at direct ETTIN targets they suggest that this protein acts as a central node for the coordination of auxin signaling in the shoot. Finally their analysis of the effect of auxin on interactions between ETTIN and other transcription factors indicates that these are important factors in the diverse set of growth process controlled by auxin.


Yang H, Berry S, Olsson TSG, Hartley M, Howard M, Dean C (2017) Distinct phases of Polycomb silencing to hold epigenetic memory of cold in Arabidopsis. Science 10.1126/science.aan1121

This is another manuscript resulting from the extremely fruitful collaboration between the labs of Caroline Dean and Martin Howard at the John Innes Centre. This paper again focuses on the FLC locus and provides evidence for a new mechanism that defines how the binding of a subset of PRC2 factors nucleates a small region (<500bp) of chromatin at the FLC TSS, causing an increase in the repressive H3K27me2 histone mark. This metastable region serves as the seed for the development of stable epigenetic marks across the length of the locus through the activity of other distinct Polycomb factors. This occurs after a cold treatment and causes the spread of H3K27me2 repression. The novelty of this work is in the distinct temporal separation of phases of silencing, which ultimately result in the repression of FLC expression after a prolonged cold treatment.


Seki M, Ohara T, Hearn TJ, Frank A, da Silva VCH, Caldana C, Webb AAR, Satake A (2017) Adjustment of the Arabidopsis circadian oscillator by sugar signalling dictates the regulation of starch metabolism. Sci Rep. 10.1038/s41598-017-08325-y

Open Access

Research from Alex Webb’s group at the University of Cambridge features in the ARR for the second consecutive week, again on a similar topic. On this occasion they collaborate with Japanese colleagues to investigate the role of the circadian clock on determining the nighttime usage rate of starch that has accumulated during the day. They used a phase oscillator model to explain the link between the speed of the clock, starch breakdown and the maintenance of sucrose homeostasis. In addition they use Arabidopsis sugar response mutants to show that the circadian clock measures amount of cellular sucrose, which then controls the dynamics of starch breakdown.


Karpinska B, Alomrani SO, Foyer CH (2017) Inhibitor-induced oxidation of the nucleus and cytosol in Arabidopsis thaliana: implications for organelle to nucleus retrograde signalling. Philos Trans R Soc Lond B Biol Sci. 10.1098/rstb.2016.0392 Open Access

Christine Foyer (University of Leeds) is the corresponding author on this paper that looks at the effect of cellular oxidation on retrograde signaling between chloroplasts, mitochondria and the nucleus. They use a novel in vivo redox reporter to measure the effect of commonly used organelle inhibitors on cellular redox state. They discovered that these inhibitors cause a variety of effects on redox state and gene expression, which differed dependent on cell type. Researchers should be aware of these effects when they are drawing conclusions from their own experiments using these inhibitors.


Wilson DC, Kempthorne CJ, Carella P, Liscombe DK, Cameron R (2017) Age-Related Resistance in Arabidopsis thaliana Involves the MADS-domain Transcription Factor SHORT VEGETATIVE PHASE and Direct Action of Salicylic Acid on Pseudomonas syringae. Mol Plant Microbe Interact 10.1094/MPMI-07-17-0172-R

Phillip Carella is a Research Fellow at SLCU and this work from this previous lab in Canada investigates Arabidopsis Age-Related Resistance (ARR), a process that requires SA accumulation, which is then thought to act as an antimicrobial agent. The ARR response is lacking in plants containing a mutation in for the SHORT VEGETATIVE PHASE (SVP) gene. These svp plants have reduced SA, thought to be due to uncoupled overactivity of the SUPPRESSOR OF OVEREXPRESSION OF CO 1 gene. Overall this study shows that the flowering time gene SVP plays a complementary role in the control of SA accumulation, which confers ARR to older plants.


Fernie AR, Bauwe H, Sweetlove LJ (2017) Investigating the Role of the Photorespiratory Pathway in Non-photosynthetic Tissues. Methods Mol Biol 10.1007/978-1-4939-7225-8_15

Lee Sweetlove (University of Oxford) describes a protocol for evaluating the role of the photorespiration on the control of growth in non-photosynthetic tissues. This can be scaled for use in both Arabidopsis and in larger plants.

Arabidopsis Research Roundup: August 14th

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Published on: August 14, 2017

This weeks UK Arabidopsis Research Roundup includes a study from the lab of GARNet Chairman Steven Spoel that describes their work on the control of ROS signaling. The other two papers looks at different aspects of photosynthetic control. Firstly Giles Johnson (University of Manchester) investigates the proteomic changes that occur during dynamic acclimation. Finally Alex Webb’s lab (University of Cambridge) investigate how the products of photosynthesis feed into ethylene-dependent control of the circadian clock.


Kneeshaw S, Keyani R, Delorme-Hinoux V, Imrie L, Loake GJ, Le Bihan T, Reichheld JP, Spoel SH (2017) Nucleoredoxin guards against oxidative stress by protecting antioxidant enzymes.

PNAS https://doi.org/10.1073/pnas.1703344114 Open Access

GARNet Chairman Steven Spoel (University of Edinburgh) leads this Franco-UK collaboration that investigated the role of the pathogen-induced oxidoreductase Nucleoredoxin 1 (NRX1) during the response to oxidative stress. They show that NRX1 targets a range of enzymes that are responsible for scavenging damaging cellular H2O2 and subsequently protect these enzymes from damage. This unexpected regulatory mechanism demonstrates a key role for NRX1 in protecting plants from the oxidative stress, which is an important component of the plants defence response.

Steven discussed this paper below. This audio is also on GARNet YouTube and iTunes channels.


Miller MAE, O’Cualain R, Selley J, Knight D, Karim MF, Hubbard SJ, Johnson GN (2017) Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome Front Plant Sci. https://doi.org/10.3389/fpls.2017.01239 Open Access

Giles Johnson leads this collaborations between two departments from the University of Manchester that has looked at changes to the leaf proteome that occur under differing light conditions. Transferring leaves from low to high light conditions causes a process called dynamic acclimation, which is perturbed in gpt2 mutants. Proteomic analysis of wildtype and gpt2 leaves reveals that a similar number of proteins are changed during dynamic acclimation but the identify of these is altered, with a reduced abundance of proteins involved in photosynthesis. Interestingly gpt2 showed an increase in the number of proteins involved in the stress response.

In 2016 Giles talked to GARNet about a different paper that looks at cold acclimation in Arabidopsis.


Haydon MJ, Mielczarek O, Frank A, Román Á, Webb AA (2017) Sucrose and ethylene signaling interact to modulate the circadian clock. Plant Physiol. https://doi.org/10.1104/pp.17.00592 Open Access

Alex Webb (University of Cambridge) collaborates with Mike Laydon (previously at York, now at the University of Melbourne) on this study that links photosynthesis with circadian and hormone signalling. Previous work showed that GIGANTEA (GI) is necessary to maintain sucrose-dependent circadian oscillations in the dark. This extension of that work demonstrates that sucrose stabilises GI by altering the activity of the ZEITLUPE (ZTL) F-box protein, which is surprisingly dependent on the key ethylene signalling intermediate CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1). Over recent times the role of ethylene on control of the circadian clock has been overlooked but this study shows that the hormone can shorten the circadian period through the activity of sucrose and GI. This study integrates another signal into our understanding of the exquisite regulatory relationships that control clock function.


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Arabidopsis Research Roundup: July 18th

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Published on: July 18, 2017

This weeks Arabidopsis Research Roundup includes four studies from around the UK. Firstly is a systems-level study of the drought response that includes Alessandra Devoto from RHUL as a co-author. Secondly Anne Osbourn’s group at the JIC investigates sesterterpenoid biosynthesis across plant species. Thirdly Paul Jarvis from Oxford University adds to this groups portfolio of research on the mechanisms that control thylakoid import. Finally Patrick Gallois (University of Manchester) provides further insight into the regulation of programmed cell death.


Kim JM, To TK et al (2017) Acetate-mediated novel survival strategy against drought in plants Nature Plants http:/​/​dx.​doi.​org/10.1038/nplants.2017.97

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Alessandra Devoto (Royal Holloway) is a co-author of this study led by Jong-Myong Kim, Mototaki Seki (RIKEN, Yokohama) and Taiko Kim Ko (University of Toyko) that investigates the system-wide alterations that plants make in response to drought stress. They demonstrate that the histone deacetylase HDA6 is the primary regulator of an epigenetic switch that leads to a metabolic flux conversion from glycolysis into acetate synthesis. This in turn stimulates the jasmonate signaling pathway that causes increased drought tolerance. Importantly the authors show that this critical survival response is evolutionarily conserved through monocots and dicots.


Huang AC, Kautsar SA, Hong YJ, Medema MH, Bond AD, Tantillo DJ, Osbourn A (2017) Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution. PNAS http:/​/​dx.​doi.​org/10.1073/pnas.1705567114

Open Access

Anne Osbourn (JIC) leads this study in which her group works with collaborators from Cambridge, Wageningen and UC Davis to perform a cross-species genome-wide analysis of sesterterpenoid biosynthesis. They use a novel search algorithm to identify paired enzymatic components that comprise sesterterpene synthases (STS). These enzymes were transiently overexpressed in tobacco leaves, resulting in the formation of fungal-like sesterterpenes, suggestive of convergent evolution of plant and fungal STS. This study illuminates possible future strategies for the beneficial use of sesterterpenes through metabolic and protein engineering


Bédard J, Trösch R, Wu F, Ling Q, Flores-Pérez Ú, Töpel M, Nawaz F, Jarvis P (2017) New Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis. Plant Cell. http:/​/​dx.​doi.​org/10.1105/tpc.16.00962 Open Access

Paul Jarvis (Oxford University) leads this global collaboration that focuses on the chloroplast protein import protein Tic40. A suppressor screen identified two novel regulators of Tic40, ALB4 and STIC2 that they postulate are involved in the thylakoid targeting of a subset of proteins and that their influence becomes more important in the absence of Tic40.


Cai YM, Yu J, Ge Y, Mironov A, Gallois P (2017) Two proteases with caspase-3-like activity, cathepsin B and proteasome, antagonistically control ER-stress-induced programmed cell death in Arabidopsis. New Phytol.

http:/​/​dx.​doi.​org/10.1111/nph.14676 Open Access

Patrick Gallois is the corresponding author on this study that originates at the University of Manchester. They attempt to establish a role for cathepsin B and proteasome subunit PBA1 in the control of programmed cell death (PCD) and whether their functions interest with those of caspase-3. They reveal a complex system of regulation where aspects of PCD are differentially impacted by each of these proteins. They propose the role of cathepsin B might occur late in PCD following tonoplast rupture.

Arabidopsis Research Roundup: July 3rd.

The Arabidopsis Research Roundup returns this week with selection of publications from institutions across the UK. Firstly George Bassel (Birmingham) leads a study that investigates the integration of inductive signals in the embryonic root. Secondly a group from the Oxford Brookes plant science group look into the literal linkages between the golgi apparatus and ER. Thirdly John Christie (Glasgow) and co-workers define a new variant of the phototropin receptor. Next Caroline Dean and Martin Howard (John Innes Centre) collaborate on work that defines the relationship between FLC, COOLAIR and cell size. The fifth paper is led by members of SLCU and investigates the regulatory influence of the Evening Complex of the circadian clock. The penultimate paper features work from Alison Smith’s group at the JIC that looks at dynamics of starch accumulation and degradation. Lastly is research from NIAB that defines the pathogeniticity of novel UK isolates of the fungal pathogen Verticillium longisporum.


Topham AT, Taylor RE, Yan D, Nambara E, Johnston IG, Bassel GW (2017) Temperature variability is integrated by a spatially embedded decision-making center to break dormancy in Arabidopsis seeds. PNAS

http:/​/​dx.​doi.​org/10.1073/pnas.1704745114

Open Access

George Bassel (University of Birmingham) leads this study that identifies a decision making centre in the embryonic root that is defined by the intimate interaction between the hormones abscisic acid (ABA) and gibberellin (GA). The activity of this ‘decision centre’ is linked to both hormone transport and changes in temperature, the overall output of which is the decision to promotes seed germination or to delay until more favourable environmental conditions.

George discusses this paper on the GARNet YouTube channel.



Osterrieder A, Sparkes IA, Botchway SW, Ward A, Ketelaar T, de Ruijter N, Hawes C (2017) Stacks off tracks: a role for the golgin AtCASP in plant endoplasmic reticulum-Golgi apparatus tethering. J Exp Bot. http:/​/​dx.​doi.​org/10.1093/jxb/erx167

Open Access

Anne Osterrieder and Chris Hawes (Oxford Brookes University) continue their work that looks at  the cellular dynamics of the golgi apparatus with this study that identifies the AtCASP protein as a important component that tethers the golgi to the ER. They use live-cell imaging to visualise golgi formation in cells that have different levels of AtCASP, allowing the authors to confirm that ER-golgi tethering is disrupted without the activity of this protein.


Petersen J, Inoue SI, Kelly SM, Sullivan S, Kinoshita T, Christie JM (2017) Functional Characterization of a Constitutively Active Kinase Variant of Arabidopsis Phototropin 1

J Biol Chem. http:/​/​dx.​doi.​org/10.1074/jbc.M117.799643

Open Access

John Christie (University of Glasgow) collaborates with Japanese colleagues to identify a novel variant of the phototropin receptor. Study of this variant allows a greater understanding regarding the mode of action of this protein under different light conditions, as controlled by phosphorylation.


Ietswaart R, Rosa S, Wu Z, Dean C, Howard M (2017) Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation. Cell Syst. http:/​/​dx.​doi.​org/10.1016/j.cels.2017.05.010

Open Access

Martin Howard and Caroline Dean (John Innes Centre) again collaborate on research that analyses the mode of regulation of FLC. They dissect RNA dynamics of FLC expression by single molecule in situ RNA fluorescence, showing that this is dependent on the presence of the antisense COOLAIR regulatory DNA. In the absence of COOLAIR they show FLC expression has a linear relationship with cell size but in the presence of the antisense transcript, FLC expression decreases with cell size. Overall they demonstrate FLC expression is tightly dependent on the presence of the antisense COOLAIR transcript.


Ezer D, Jung JH, Lan H, Biswas S, Gregoire L, Box MS, Charoensawan V,, Cortijo S, Lai X,, Stöckle D, Zubieta C, Jaeger KE, Wigge PA (2017) The evening complex coordinates environmental and endogenous signals in Arabidopsis. Nat Plants.

http:/​/​dx.​doi.​org/10.1038/nplants.2017.87

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Phil Wigge and Katja Jaeger (SLCU) lead this study that investigates how the evening complex of the circadian clock coordinates the expression of numerous important growth regulators. This genome wide regulation is determined by temperature and concides with the binding of phytochrome B, which provides a cellularly mechanism of this level of environmental control.


Fernandez O, Ishihara H, George GM, Mengin V, Flis A, Sumner D, Arrivault S, Feil R, Lunn JE, Zeeman SC, Smith AM, Stitt M (2017) Foliar starch turnover occurs in long days and in falling light at the end of the day. Plant Physiol. http:/​/​dx.​doi.​org/10.1104/pp.17.00601

Open Access

On this paper Alison Smith (John Innes Centre) is a co-corresponding author together with Mark Stitt from the Max Planck Institute for Molecular Plant Physiology in Potsdam. They continue their work to investigate the dynamics of starch metabolism in Arabidopsis leaves. Broadly they show the rate of starch accumulation corresponds to the photosynthetic rate whilst degradation is linked to correct functioning of the circadian clock. They investigate this process in more detail by determining how the rate of starch degradation alters dependent on the time after dawn.


Depotter J, Rodriguez-Moreno L, Thomma BP, Wood T (2017) The emerging British Verticillium longisporum population consists of aggressive Brassica pathogens. Phytopathology http:/​/​dx.​doi.​org/10.1094/PHYTO-05-17-0184-R

Tom Wood (NIAB) is the corresponding author of this study that characterises four new UK isolates of the fungal pathogen Verticillium longisporum. The pathogenticity of V.longisporum was tested on Arabidopsis alongside three other Brassica crops. They demonstrate that the UK isolates were unusually aggressive yet this was not consistent across all Brassica cultivars with different fungal lineages showing different effects on oil seed rape, cabbage or cauliflower.

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.

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.

Passing the threshold gives a Giant output!

Categories: Cambridge University
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Published on: February 23, 2017

A recent Arabidopsis Research Roundup included a paper from Adrienne Roeder’s lab in Cornell that includes James Locke and Henrik Jonsson from SLCU. The research focuses on the Arabidopsis sepal, which has been the central theme of the Roeder lab since it was set up a few years ago. On a personal level I recall seeing a talk on this topic maybe 10 years ago and it’s always struck me as a fantastically simplistic system that can be used to answer some fundamental questions about the processes that control cell patterning.

This latest paper is focused on the important question of how adjacent cells are set on different development paths, using the giant sepal cells as an excellent model system. This type of cell type specificity is thought to develop following mild stochastic fluctuations in gene expression that lead into feedback loops that accentuate these initial differences. However this has not yet been visualized in vivo until this new manuscript in Elife

The sepal is the outermost organ of the Arabidopsis flower and its correct shape relies on the formation of giant epidermal cells that can grow up to 20% of the entire organ length. These are necessary for the correct function of the organ (to facilitate flower opening) and they form in approximately equal numbers to non-giant cells. Prior to this paper the mechanism of this patterning remained opaque as giant cells can form either adjacent to or apart from each other. The ATML1 transcription factor plays an important role in general Arabidopsis epidermal patterning and has been shown to be required for the generation of giant sepal cells. Importantly the increased size of these giant cells is facilitated by rounds of endoreduplication that can result in 64C nuclei.


ATML1 is expressed in all sepal cells yet only a subset of these will become giant. By using ATML1-overexpression lines together with a simple genetic analysis, the authors show that gene dosage of the ATML1 gene determines the number of giant cells that form (constitutive ATML1 expression have all giant cells). The mechanism by which this dosage results in a mixed cell fate was unclear until they found (using a line containing a fluorescent ATML1-Citrine protein) that ATML1 expression fluctuated far more in the sepal cells than did other genes expressed in the same tissue.

The authors used some fantastic live imaging to show that there are high levels of ATML1 expression in cells destined for giant fate. Although this was not an absolute relationship (as some smaller cells also showed high ATML1 expression), they mathematically demonstrate that obtaining a high threshold of ATML1 correlated about 70% of the time with uptake of giant cell fate.

Finer detail was added to this picture when it became clear that obtaining this threshold at a particular phase of the cell cycle was much more strongly correlated with giant-cell fate. If this threshold is obtained when DNA content was 4C (occurring after DNA replication in G2 phase of the cell cycle) then in 80% of the time the cell became giant. As the authors state ‘a cell is competent to respond to high levels of ATML1 mainly during G2 to induce giant cell formation’.


Finally the authors used plants with a mutation in the LGO gene (LOSS OF GIANT CELLS FROM ORGANS), which have sepals with no giant cells, to determine whether there was feedback control of ATML1 once giant cell fate had been determined. The lgo mutant is epistatic to atml1 and consistent with this observation they show that ATML1 fluctuates normally in the lgo mutant but that this signal does not lead to endoreduplication and giant cell formation. Therefore there is no feedback loop that features endoreduplication and ATML1; rather there is a linear mechanism in which ATML1 fluctuations set in motion endoreduplication, which then continues independent of those ongoing fluctuations.

 

This data was then used to develop a model that could precisely predict the location of giant cell formation based on this information about rapid yet relatively small fluctuations in ATML1 levels.
  Overall this study is an outstanding example of using technological advances in live imaging in a simple experimental system to help develop an understanding of a complex regulatory system. It remains to be seen whether this type of threshold-fluctuation model is important for patterning in other tissues. However this case is an scientific tour of force, demonstrating what is possible when technical advances are put together with careful measurements and inspired experimental planning!

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