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  • geraintparry
  • GARNet Coordinator @ Cardiff University. Past lecturer in Plant Science and genetics. Researcher into plant nuclear transport and regulation of auxin signalling.

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GARNet Gene Editing Workshop!

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Published on: February 12, 2018

GARNet with support from the Bristol Centre for Agricultural Innovation and New Phytologist are organising a Gene Editing Workshop that will take place at the University of Bristol on March 26th-27th 2018.

This workshop is designed to encourage interactions and discussion about the use of CRISPR-Cas9 gene editing in plant systems.

We are encouraging ECRs to attend the meeting and are providing nine opportunities for talks by people who have submitted abstracts. We are also hosting extended poster sessions.

The workshop has three main plenary sessions that will look at the technical aspects of using GE in different plant species. In addition we are hosting a session with a extended opportunity for debate regarding the policy decisions that surround use of this technology.

The full workshop schedule is here: https://garnet-ge-workshop.weebly.com/schedule.html

Monday 26th March
Opening Plenary: Stefan Jansson (Umea): Cooking (and eating) the first gene-edited meal!

Session I: Gene Editing in Dicots
Session II: Gene Editing in Monocots

Keynote Plenary: Ben Davies: Transgenic Core Head, Wellcome Trust Centre for Human Genetics, University of Oxford.

Tuesday 27th March

Session III: Gene Editing and Global Regulatory Landscape
Session IV: Novel uses of gene editing technologies

Registration for this workshop is now open and only costs £65 for ECRs.

As we are keeping the meeting small there is only space for 100 delegates!
Please register early to avoid disappointment.

We have arranged options for budget hotel accommodation for delegates in Bristol so please take advantage of these offers here:

The abstract submission deadline to be considered for talks and posters is March 1st.

Please send your abstracts to the GARNet coordinator Geraint Parry at geraint@garnetcommunity.org.uk

Thanks to the High Value Chemical from Plants network for providing additional support.

Henrik Jonsson and Benoit Landrien talk to GARNet

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Published on: February 7, 2018

Henrik Jonsson and Benoit Landrien discuss their new PNAS paper entitled ‘Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins‘.
Grafting image taken from Charles Melynk

Bumping into a hole understanding of auxin signaling

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Published on: January 24, 2018

The cellular mechanics of auxin perception and signaling have been well studied over the past two decades. The pivotal interaction that controls this activity involves the auxin-dependent contact between the TIR1 receptor and a family of transcriptional regulators called AuxIAA proteins. This interaction has been characterised at a structural level with the auxin indole-3-acetic acid (IAA) shown to act as a ‘molecular glue’, stabilising the interaction between TIR1 and the AuxIAA. This subsequently causes the degradation of the AuxIAA protein, setting off a cascade of auxin-dependent transcriptional responses.

Revealing the precise kinetics of this interaction is complicated by the fact that TIR1 belongs to a family of six related receptors and the AuxIAA family comprises 29 members. Although IAA is able to mediate the interaction between each of these family members, the TIR1 auxin binding pocket is somewhat promiscuous, with a wide range of auxin analogues being able to illicit a similar responses.

In order to develop a synthetic auxin signaling complex that was free from the complexities of varying protein family interactions, Keiko Torii and co-workers from the University of Washington and Nagoya University employed a bump-and-hole strategy. This technique sits at the interface of chemistry, biology and engineering and in this case was able to create a functional synthetic receptor-substrate interaction that did not interfere with the endogenous activity of TIR1-AuxIAA. This research has been published in Nature Chemical Biology.


Using the bump-and-hole strategy the authors interrogated the TIR1 auxin binding-pocket, predicting that removal of a bulky phenylalanine would result in a ‘hole’ whose space could be filled by a version of IAA that included an aryl-ring ‘bump’.

The authors showed that this ‘concave (ccv) TIR1’ was able to interact with the ‘convex (cvx) IAA’ and remarkably be able to elicit a biological relevant response in vivo. Generation of transgenic plants expressing ccvTIR1 or the application of exogenous cvxIAA has little effect on plant growth. However in the presence of cvxIAA, these ccvTIR1 transgenic plants show alterations in primary root elongation, lateral root development and gene expression changes characteristic of an auxin response. Therefore this paper synthetically replicated the auxin signaling module, whose function absolutely relies upon the presence of both components.

This research is a superb example for the use of modeling and synthetic chemistry to facilitate the study of a complex biological system. There is no doubt that the ccvTIR1-cvxIAA system is an important tool for study of the cellular auxin response as well for the tissue-specific activities of this do-it-all phytohormone. We await the development of an engineered enzyme that can produce cvxIAA in vivo so that the system will not need to rely on any external additions!!!

Arabidopsis Research Roundup: January 23rd.

This weeks Arabidopsis Research Roundup begins with two papers from Royal Hollaway University of London that investigate the factors that control leaf development in the dark and the control of PIN1 phosphorylation. Third is a paper from Bristol that demonstrates the translation of research from Arabidopsis into coriander with regard the control of the response to UV light. Next is research from the John Innes Centre that characterises the role of DNA methylation during meiosis in the male lineage.

Christine Foyer (Leeds) leads the next paper that defines the relationship between cold treatment and strigolactone signalling. The penultimate paper is led by Richard Napier from the University of Warwick and determines the parameters that define the substrates of the AUX1 protein whilst the final paper includes Cyril Zipfel (TSL) as a co-author and uses systems biology approaches to characterise the interactions between leucine-rich repeat receptor kinases (LRR-RKs).

Mohammed B, Farahi Bilooei S, Doczi R, Grove E, Railo S, Palme K, Ditengou FA, Bögre L, Lopez-Juez E (2017) Converging energy and hormonal signalling control meristem activity, leaf initiation and growth Plant Phys doi: 10.1104/pp.17.01730


Open Access

Enrique Lopez-Juez (RHUL) leads this collaboration with German and Hungarian colleagues that investigates the fundamental question; ‘Why don’t leaves grow in the dark’. They show that this response is influenced by both auxin transport and the plants energy sensing mechanisms. Interestingly when energy is provided via external sucrose, leaves develop differently in the dark than they do in the light indicating that multiple signaling pathways differentially influence this phenotype.

Enrique discusses this paper on the GARNet YouTube page.

Dory M, Hatzimasoura E, Kállai BM, Nagy SK, Jäger K, Darula Z, Nádai TV, Mészáros T, López-Juez E, Barnabás B, Palme K,,, Bögre L, Ditengou FA,,, Dóczi R (2017) Coevolving MAPK and PID phosphosites indicate an ancient environmental control of PIN auxin transporters in land plants. FEBS Lett. doi: 10.1002/1873-3468.12929

Laszlo Bogre and Enrique Lopez-Juez (RHUL) are co-authors on this Hungarian-led study that has discovered 3 conserved putative MAPK sites within the auxin transport protein PIN1. Phosphorylation of two of these sites causes partial loss of PIN1 membrane localization and therefore opposes the effect of the PINOID kinase, whose activity promotes PIN1 membrane localisation.


Fraser DP, Sharma A, Fletcher T, Budge S, Moncrieff C, Dodd AN, Franklin KA (2017) UV-B antagonises shade avoidance and increases levels of the flavonoid quercetin in coriander (Coriandrum sativum). Sci Rep. doi: 10.1038/s41598-017-18073-8 Open Access

Keara Franklin and Anthony Dodd (University of Bristol) lead this collaboration between academic researchers and those in the company Vitacress. They translate research from Arabidopsis into Coriander that looks at the effect of UV-B on stem elongation and the interaction with flavonoid signaling. This work shows that alterations to the UV-B regime during growth of potted herbs might reduce deleterious effects caused by neighbour proximity.

Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X (2017) Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nat Genet. doi: 10.1038/s41588-017-0008-5

Xiaoqi Feng (JIC) is the corresponding author on this collaboration with James Higgins from Leicester and they investigate the role of DNA methylation in the control of male meiosis. They demonstrate that RNA-directed DNA methylation (RdDM) in the male lineage regulates gene expression in meiocytes and results in the mis-splicing of the MPS1/PRD2 transcipt, which causes aberrant alterations in spindle formation.

Cooper JW, Hu Y, Beyyoudh L, Yildiz Dasgan H, Kunert K, Beveridge CA, Foyer CH (2018) Strigolactones positively regulate chilling tolerance in pea and in Arabidopsis. Plant Cell Environ. doi: 10.1111/pce.13147

Christine Foyer (Leeds) is the corresponding author on this collaboration with Australian, Turkish and South African colleagues that looks into the role strigolactones play during chilling tolerance in both Arabidopsis and pea plants. Plants that have been chilled during the night have reduced biomass, which was not observed in either pea or Arabidopsis strigolactone mutants. This demonstrates a clear role for this hormone in this response and provides a potential target for the manipulation of plant growth under environmental conditions.

Hoyerova K, Hosek P, Quareshy M, Li J, Klima P, Kubes M,, Yemm AA, Neve P, Tripathi A, Bennett MJ, Napier RM (2017) Auxin molecular field maps define AUX1 selectivity: many auxin herbicides are not substrates. New Phytol. doi: 10.1111/nph.14950


Together with Czech co-authors Richard Napier (Warwick University) leads this investigation into the mode of action of the AUX1 auxin influx carrier and its substrate preferences. This work made use of a novel auxin accumulation assay and associated mathematical modeling to describe the parameters that make difference auxins to be good candidates for the AUX1 transport. Interesting they find that many commonly used auxinicide herbicides are poor substrates for AUX1 and the relevance of this finding for herbicide management strategies.


Smakowska-Luzan E et al (2018) An extracellular network of Arabidopsis leucine-rich repeat receptor kinases. Nature doi: 10.1038/nature25184

Cyril Zipfel (TSL) is a co-author on this US-European study that performs a systems-biology analysis on the possible interactions between extracellular domains of the leucine-rich repeat receptor kinases (LRR-RKs) gene family in Arabidopsis. Analysis of 40K potential interactions allows the generation of a LRR-based cell surface interaction network (CSI-LRR). This was used to discover previously uncharacterized interactions between LRR-RKs and to demonstrate that these interactions allow the translocation of extracellular signals in balanced and tightly regulated patterns.

Enrique Lopez-Juez (RHUL) talks to GARNet

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Published on: January 17, 2018

Enrique Lopez-Juez (Royal Holloway University of London) introduces a paper from that attempts to answer a critical question in plant science ‘Why do plants makes leaves in the dark‘?



Arabidopsis Research Roundup: January 10th 2018

This Arabidopsis Research Roundup covers the final papers of 2017 and the first of this new year. The initial paper is led by researchers in Bristol and characterises how the multifaceted BIG protein influences stomatal dynamics in response to altered CO2. Second is a manuscript from SLCU that for the first time in plants demonstrates nuclear sequestration of cell cycle regulated mRNAs.

Next is a paper from Rothamsted that describes a role for the hormone GA during floral development. David Salt (Nottingham) is then a co-author on a manuscript that has determined a role for the CTL protein in ion homeostasis.

Seth Davies from York is the lead author on the next study that investigates a link between metabolism and the circadian clock. The sixth paper looks at genes involved in the control of autophagy and features Patrick Gallois (Manchester) as a co-author.

There are three papers from researchers working on Norwich Research Park with Cyril Zipfel (TSL) involved in a study that looks at vacuolar trafficking of BR signaling components. Janneke Balk leads a study that characterises enzymes involved in biosynthesis of metal co-factors whilst the final NRP-based paper from Nick Pullen and Steven Penfield (John Innes Centre) describes the Leaf-GP open software for automated plant phenotyping.

The penultimate paper uses a set of PlantProbes (developed by Paul Knox at Leeds) to study pollen development whilst the final paper from Keith Lindsey (Durham) describes the application of a Bayesian statistical methodology to model the parameters that control a hormone signaling network.

He J, Zhang RX, Peng K, Tagliavia C, Li S, Xue S, Liu A, Hu H,, Zhang J, Hubbard KE,, Held K, McAinsh MR, Gray JE, Kudla J, Schroeder JI, Liang YK, Hetherington AM (2018) The BIG protein distinguishes the process of CO2 -induced stomatal closure from the inhibition of stomatal opening by CO2. New Phytol. doi: 10.1111/nph.14957 Open Access

Alistair Hetherington (University of Bristol) leads this UK-USA-China collaboration that has characterised a role for the mysterious BIG protein during stomatal closure in response to altered CO2 concentration. Interestingly BIG mutants do not show a defect in stomatal opening in response to altered CO2, allowing the dissection of this complex response through the activity of this protein. It remains to be determined exactly how the BIG protein influences this process.

Yang W, Wightman R, Meyerowitz EM (2017) Cell Cycle Control by Nuclear Sequestration of CDC20 and CDH1 mRNA in Plant Stem Cells. Mol Cell. doi: 10.1016/j.molcel.2017.11.008

Elliott Meyerowitz (SLCU) is the corresponding author of this research that provides the first characterisation in plants of nuclear sequestration of mRNAs from developmental important genes. The authors show that Arabidopsis anaphase-promoting complex/cyclosome (APC/C) coactivator genes CDC20 and CCS52B are confined to the nucleus in prophase, preventing translation of the cognate proteins until metaphase, which appears to protect cyclins from degradation at an inappropriate phase of the cell cycle

Plackett ARG, Powers SJ, Phillips AL, Wilson ZA, Hedden P, Thomas SG4 (2017) The early inflorescence of Arabidopsis thaliana demonstrates positional effects in floral organ growth and meristem patterning. Plant Reprod. doi: 10.1007/s00497-017-0320-3

This study is led from Rothamsted Research and includes Zoe Wilson from the University of Nottingham. They perform a systematic analysis of early floral organ initiation across the Arabidopsis inflorescence, discovering that both GA-dependent and independent stages are important for this process, albeit via the activity of presently unknown factors.

Gao YQ, Chen JG, Chen ZR An D, Lv QY, Han ML, Wang YL, Salt DE, Chao DY (2017) A new vesicle trafficking regulator CTL1 plays a crucial role in ion homeostasis. PLoS Biol. doi: 10.1371/journal.pbio.2002978

Open Access

David Salt (University of Nottingham) is a co-author on this Chinese-led investigation into the role of the vesicle trafficking regulator choline transporter (CTL) during the control of ionome homeostasis. Using ctl1 mutants they show that this function is required for the action of certain ion transporters as well as during plasmodesmata (PD) development. This study provides novel insights into the role of vesicular transport in the control of ion homeostasis and how the location of these ions might alter vesicle activity.

Sánchez-Villarreal A, Davis AM, Davis SJ (2017) AKIN10 Activity as a Cellular Link Between Metabolism and Circadian-Clock Entrainment in Arabidopsis thaliana.

Plant Signal Behav. doi: 10.1080/15592324.2017.1411448

Seth Davies (University of York) is the corresponding author on this study demonstrating that overexpression of the AKIN10 subunit of the SnRK1 complex results in increased period length of the circadian clock. The authors postulate about the possible links between metabolic rate and function of the clock, allowing them to present a model of action that features each of the central regulatory elements.

Havé M, Balliau T, Cottyn-Boitte B, Dérond E, Cueff G, Soulay F, Lornac A, Reichman P, Dissmeyer N, Avice JC, Gallois P, Rajjou L, Zivy M, Masclaux-Daubresse C (2017) Increase of proteasome and papain-like cysteine protease activities in autophagy mutants: backup compensatory effect or pro cell-death effect? J Exp Bot. doi: 10.1093/jxb/erx482

Open Access
This study is led by French researchers and includes Patrick Gallois (University of Manchester) as a co-author. The work focuses on the role of the ATG genes during autophagy, the key process that controls nutrient recycling during senescence. In atg5 mutants they show that different sets of proteases are misregulated, suggestive of a complex relationship between the enzymes involved in nutrient remobilization.

Liu Q, Vain T, Viotti C, Doyle SM, Tarkowská D, Novák O, Zipfel C, Sitbon F, Robert S, Hofius D (2017) Vacuole Integrity Maintained by DUF300 Proteins Is Required for Brassinosteroid Signaling Regulation. Mol Plant. doi: 10.1016/j.molp.2017.12.015

Cyril Zipfel (TSL) is a member of this Pan-European consortium that investigates the role of the vacuolar proteins, LAZARUS1 (LAZ1) and LAZ1 HOMOLOG1 (LAZ1H1) on the cellular cycling of BR-signaling components. Plants with mutations in laz1 and laz1h1 show increased BAK1 accumulation at the tonoplast as well as enhanced BRI1 trafficking and degradation. These DUF300 proteins appear to play a specific role in BR signalling as other vacuolar-associated proteins are not involved in this process.

Kruse I, Maclean A, Hill L, Balk J (2017) Genetic dissection of cyclic pyranopterin monophosphate biosynthesis in plant mitochondria. Biochem J. doi: 10.1042/BCJ20170559 Open Access

Janneke Balk (John Innes Centre) leads this study that has identified novel alleles in mitochondrial enzymes that are involved in the biosynthesis of metal cofactors. Analysis of these enzyme mutant reveals that they show deficiencies in the synthesis of cyclic pyranopterin monophosphate (cPMP), revealing fresh insights into the metabolic processes involving this key intermediate.

Zhou J, Applegate C, Alonso AD, Reynolds D, Orford S, Mackiewicz M, Griffiths S, Penfield S, Pullen N (2017) Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat. Plant Methods. doi: 10.1186/s13007-017-0266-3

Open Access

Nick Pullen and Steve Penfield (John Innes Centre) introduce this new software tool for the automated measurement of plant phenotypes. This Leaf-GP software is open access and has the sophistication to discriminate between different aspects of both Arabidopsis and greenhouse growth wheat.

This paper is back of a special issue of Plant Methods that is based on the use of Computer Vision in Plant Phenotyping.

Ndinyanka Fabrice T, Vogler H, Draeger C, Munglani G, Gupta S, Herger AG, Knox JP, Grossniklaus U, Ringli C (2017) LRX Proteins play a crucial role in pollen grain and pollen tube cell wall development. Plant Physiol. doi: 10.1104/pp.17.01374

Open Access

This Swiss-led study looks into the role of LRX proteins during cell wall formation and how they affect pollen germination and pollen tube formation. The authors took advantage of the molecular tools produced by Paul Knox (University of Leeds) as part of his Plant Probes project.

Vernon I, Liu J, Goldstein M, Rowe J, Topping J, Lindsey K (2017) Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions. BMC Syst Biol. doi: 10.1186/s12918-017-0484-3 Open Access

Keith Lindsey (University of Durham) leads this paper that applies a Bayesian statistical methodology to analyse a model of hormonal crosstalk in the Arabidopsis root. They show that this technique can provide new insight into the behavior of models and enables the identification of new interesting rate parameters.

Magnetising Pollen to break the Plant Transformation Bottleneck?

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Published on: December 19, 2017

The potential for crop improvement by ‘traditional’ genetic modification and by ‘game-changing’ gene-editing technologies is easy to appreciate. The introduction a foreign gene or the alteration of endogenous gene function in order to modify the way in which a plant responds to a particular environmental stimuli is the underlying goal of most applied plant scientists. Our improved knowledge of how these techniques work, advances in the speed and cost DNA synthesis alongside the adoption of the principles of synthetic biology in the engineering of molecular constructs means that generation of DNA parts for genetic modification is, in theory at least, now facile endeavor.

However there is an ‘eleplant in the room’ of every grant proposal that promises to generate an altered variety of any desired orphan crop. Our ‘eleplant’ is the efficiency, or lack thereof, in plant transformation. This issue was the topic of a 2016 Perspective piece in The Plant Cell in which the example of Sorghum was cited, an important food crop that is unfortunately recalcitrant to transformation, taking up to 12months to generate T1 transformants. This bottleneck will continue to be an issue when discussing new targets for genetic modification as callus-based mechanisms of transformation are famously extremely challenging, with one method good for the goose might be not so good for the gander.

From http://www.plantcell.org/content/28/7/1510

These challenges have been solved for many major crops but even with this knowledge, regeneration of transgenic crops only usually takes place in labs with specific knowledge and experimental pipelines (in the UK at facilities at NIAB or the JIC)*.

It is in this climate that a recent paper by Zhao et al in Nature Plants might be another true game changer. They have modified the magnetofection procedure that has been used very successfully to introduce DNA into animal cells in order to modify existing pollen transformation techniques. This protocol involves mixing DNA with magnetic nanoparticles that can be introduced using a magnetic field into pollen grains through small apertures in the pollen wall. These transformed pollen can then be used to fertilise emasculated plants as normal, from which transgenic seeds can then be selected in the usual manner.

From https://www.nature.com/articles/s41477-017-0072-y

This technique relies upon the pollen aperature being greater than 5um and Zhao et al demonstrate that this was possible in a range of flowering plants including pepper, pumpkin, zucchini and lily. The majority of their experimental work highlighted the introduction of a gene expressing BT toxin into cotton and the subsequent identification of insect resistant plants. The viability of magnetotransformed pollen was unaffected and after the initial fertilization the transgene segregated with normal mendelian ratios.

Importantly for future uptake of this technology, the authors were able to successfully transform Elite varieties that are recalcitrant to callus-transformation, thus greatly reducing the time usually needed for crossing between easily transformable and elite lines. Success rates even for floral dip transformation are lower than 1% so the reported 2-10% in this study, over three years of experiments, strongly suggests that this technique has enormous potential for crop genetic modification.

The only minor drawback is that due to the high success rate, extra generations of selfing transgenic plants might be necessary to obtain pure breeding lines due to the integration of multiple independent insertions.

These experiments have been conducted with a single research lab so it remains to be seen whether these success rates are recapitulated in other locations that have similar but potential significant alterations in their experimental setup.

Importantly the authors do not attempt to use this technique to transform any grass species, a taxonomic group that supplies the vast majority of global animal calories. This will be important to ascertain yet might prove challenging or impossible due to the size of grass pollen grains. Only time will tell whether this is possible.

There is little doubt that this work will raise significant interest in academic and industrial labs across the globe.

Watch this space whether this will prove the breaking of the transformation bottle(neck).

*- Of course Arabidopsis is immune from such concerns as it can be transformed by floral dip, due to an unusually open gynoecium during development.

A commentary article on the Zhao et al paper is also available in Nature Plants.

Arabidopsis Research Roundup: December 18th

This festive Arabidopsis Research Roundup begins with a commentary article from a global consortium of plant scientists who propose a framework of future training for researchers who will take advantage of the experimental tools available in Arabidopsis. Secondly is study from Caroline Dean (JIC) that defines the role of the LHP1 protein in epigenetic control of gene expression. Thirdly John Doonan (Aberystwyth) is a co-author of work that defines an important component of mitotic spindle formation. Next is a study led by Zinnia Gonzalez-Carranza in Nottingham that offers further insights into the function of the HWS gene. The fifth study comes from the lab of Alexander Ruban (QMUL), further investigating the importance of NPQ in photosynthetic control. The sixth paper from the Van Ooijen lab (Edinburgh) characterises the role of sumoylation in the control of CCA1 activity. The penultimate paper from the Harberd lab in Oxford defines the importance of DNA mismatch repair on genome sequence integrity whilst the final paper characterises the next phase in the long story of Arabidopsis ALF4 function and includes Charles Melynk (SLCU) as a co-author.

Friesner J et al (2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol. doi: 10.1104/pp.17.01490. Open Access

The current GARNet PI Jim Murray and past GARNet coordinator Ruth Bastow are authors in this international consortium that suggests future directions for the global Arabidopsis community. This consortium is led by Joanna Friesner and concludes that it is critical that the next generation of plant scientists receive appropriate training in bioinformatics and quantitative biology so as to take advantage of the remarkable array of datasets that are now available to Arabidopsis researchers.

Berry S, Rosa S, Howard M, Bühler M, Dean C (2017) Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression Genes Dev. doi: 10.1101/gad.305227.117 Open Access

Caroline Dean (John Innes Centre) leads this study that investigates the role of the polycomb associated protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) in the regulation of the repressive histone mark H3K27me3. They demonstrate that the intrinsically disordered hinge region of LHP1 is responsible for RNA-binding and that disruption of this region prevents the formation of sub-nuclei foci, provides a potential link to wider epigenetic regulation.

Lee YJ, Hiwatashi Y, Hotta T, Xie T, Doonan JH, Liu B (2017) The Mitotic Function of Augmin Is Dependent on Its Microtubule-Associated Protein Subunit EDE1 in Arabidopsis thaliana. Current Biol. doi: 10.1016/j.cub.2017.11.030

Open Access

John Doonan and colleagues at Aberystwyth University are co-authors on this study regarding the role of the Microtubule-Associated Protein Subunit EDE1, which is a member of the Augmin complex, during mitosis. EDE1 specifically localised with the augmin complex during spindle formation, a role that cannot be replaced by the homologous protein AUG8. This work reveals that specificity of the augmin complex can be determined by interaction with subunits that only contribute to complex function during particular phases of the cell cycle.

Zhang X, Jayaweera D, Peters JL, Szecsi J, Bendahmane M, Roberts JA, González-Carranza ZH (2017) The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT is a new player in the microRNA pathway. PLoS One. doi: 10.1371/journal.pone.0189788 Open Access

Zinnia Gonzalez-Carranza (Nottingham) is the corresponding author on this study that follows on from work published earlier in 2017 regarding the role of the HAWAIIAN SKIRT gene is plant development. In this latest work they identify mutations in the previously characterized Exportin-5 HASTY gene as suppressors of the hws mutant phenotype. Further investigation shows that HWS genetically interacts with other genes involved in miRNA pathway indicates that HWS somehow interacts with biogenesis, accumulation or function of these small RNAs.

Townsend AJ1, Ware MA1, Ruban AV (2017) Dynamic interplay between photodamage and photoprotection in photosystem II. Plant Cell Environ doi: 10.1111/pce.13107

In this paper Alexander Ruban (QMUL) is the corresponding author on work that expands his groups contribution to the understanding of the role non-photochemical quenching (NPQ) plays during photoinhibition. In this work they compare the activity of NPQ versus endogenous photosystemI repair mechanisms in the maintenance of photosynthetic activity during photoinhibitory conditions. Overall they conclude that NPQ is a more important mechanism for photoprotection under short periods of illumination.

Hansen LL, Imrie L, Le Bihan T, van den Burg HA, van Ooijen G (2017) Sumoylation of the Plant Clock Transcription Factor CCA1 Suppresses DNA Binding. J Biol Rhythms doi: 10.1177/0748730417737695 Open Access

This paper from the Van Ooijen lab accompanies one that was featured in last weeks ARR and extends their finding that sumoylation plays an important role in control of the circadian clock. In this paper they show that the CCA1 clock protein is sumoylated and that perturbing this modification alters the binding of CCA1 to a target promotor, even though it’s localization or stability were unaffected. Using an in vitro system they show that sumoylation is a direct determinant of CCA1 binding to its target promotor suggesting that this PTM fine tunes the activity of this key circadian control element.

Belfield EJ, Ding ZJ, Jamieson FJC, Visscher AM, Zheng SJ, Mithani A, Harberd NP (2017) DNA mismatch repair preferentially protects genes from mutation. Genome Res. doi: 10.1101/gr.219303.116

Past GARNet Advisory board member Nick Harberd (Oxford) leads this multi-generational study on the effect of DNA mismatch repair (MMR) on maintenance of an entire genome. They perform whole genome sequencing across five generations of Arabidopsis plants with a mutation in the MMR pathway and show that particular types of nucleotide error are more prevelant amongst the total 9000 mutations that accumulate. Interestingly they show that single nucleotide variants are more likely to accumulate in genic regions, indicating that protein coding areas of the genome are preferentially protected from damage.

Bagchi R, Melnyk CW, Christ G, Winkler M,, Kirchsteiner K, Salehin M, Mergner J, Niemeyer M, Schwechheimer C, Calderón Villalobos LIA, Estelle M (2017) The Arabidopsis ALF4 protein is a regulator of SCF E3 ligases. EMBO J. doi: 10.15252/embj.201797159

During his time as a research fellow at the Sainsbury lab in Cambridge. Charles Melynk contributed to this research that is a throwback to the early day of Arabidopsis mutant analysis. The alf4 was first described as a possible auxin mutant in 1995 and this work brings this study full circle by characterising the ALF4 protein as a novel regulator of SCF complexes, which are known to be involved in auxin and GA signaling. ALF4 specifically functions by interacting with the SCF-core component RBX1. Future work will determine whether this effect is specific to SCFs involved in hormone signaling or whether it is a more general effect.

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