Arabidopsis Research Roundup: September 27th 2016

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

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

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

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


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

http://dx.doi.org/10.1080/19491034.2016.1236166

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

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

http://dx.doi.org/10.1371/journal.pgen.1006298 Open Access

Current GARNet Chair David Salt (then Aberdeen but recently moved to CPIB in Nottingham) leads this collaboration between UK, US and German researchers that identifies the MORE SULPHUR ACCUMULATION1 (MSA1) protein, which regulates sulphur homeostasis. MSA1 is nuclear localised, is required for S-adenosylmethionine (SAM) production and DNA methylation whilst is essential for the response to sulphur. Therefore the authors show that MSA1 appears to sit at an important control point as the plant responds to sulphur by regulating SAM biosynthesis and genome-wide DNA methylation.
MSA1pic

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

http://dx.doi.org/10.1104/pp.16.01192 Open Access

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

Toolkit for the Gene Editing of Chromosomal Deletions.

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Published on: September 20, 2016

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

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

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

 

vectors-summary-scheme.png__510x500_q85_subsampling-2_upscale

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

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

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

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

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

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

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

Arabidopsis Research Roundup: September 19th.

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Published on: September 18, 2016

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

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

Üstün S, Sheikh A, Gimenez-Ibanez S, Jones AM, Ntoukakis V, Börnke F (2016) The proteasome acts as a hub for plant immunity and is targeted by Pseudomonas type-III effectors Plant Physiology http://dx.doi.org/10.1104/pp.16.00808

Open Access

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

Craddock CP, Adams N, Kroon JT, Bryant FM, Hussey PJ, Kurup S, Eastmond PJ (2016) Cyclin-dependent kinase activity enhances phosphatidylcholine biosynthesis in Arabidopsis by repressing phosphatidic acid phosphohydrolase activity Plant Journal http://dx.doi.org/10.1111/tpj.13321 Open Access

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

Paultre DS, Gustin MP, Molnar A, Oparka KJ (2016) Lost in transit: long-distance trafficking and phloem unloading of protein signals in Arabidopsis homografts Plant Cell http://dx.doi.org/10.1105/tpc.16.00249

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

Fourquin C, Beauzamy L, Chamot S, Creff A, Goodrich J, Boudaoud A, Ingram G (2016) Mechanical stress mediated by both endosperm softening and embryo growth underlies endosperm elimination in Arabidopsis seeds Development. 143(18):3300-5. http://dx.doi.org/10.1242/dev.137224

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

EURISCO: the EU Plant Genetic Resource Catalogue

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Published on: September 15, 2016

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

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

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

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

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

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

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

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

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

Arabidopsis Research Roundup: September 13th.

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Published on: September 13, 2016

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

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

http:/​/​dx.​doi.​org/


LAX3pic
Malcolm Bennett (CPIB) is the corresponding author of this study that includes authors from the UK, USA, France, Portugal, The Netherlands, Switzerland, Austria and Japan. This manuscript adds further layer of complexity to our understanding of the factors that promote lateral root development, focussed on the role of the influx carrier LAX3 to concentrate auxin into cell layers overlying lateral root primordia. This study demonstrates that the auxin response factor ARF7 upregulates the LBD29 TF that in turn directly binds the LAX3 promotor. Disrupting the dynamics of wildtype LBD29 binding to the LAX3 promotor phenocopies the lax3 mutant, functionally demonstrating the ARF7-LBD29-LAX3 signalling module.

 

 

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

Open Access

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

 

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

Open Access

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

 

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

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

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

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

Arabidopsis Research Roundup: August 26th

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Published on: August 26, 2016

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

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

http:/​/​dx.​doi.​org/10.1371/journal.ppat.1005790

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

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

 

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

http:/​/​dx.​doi.​org/10.1371/journal.pone.0160694

Open Access

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

 

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

http:/​/​dx.​doi.​org/10.1007/s11103-016-0522-3

Open Access

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

Arabidopsis Research Roundup: August 19th

This weeks Arabidopsis Research Roundup includes broad representation from Norwich Research Park with Caroline Dean, Enrico Coen and Cyril Zipfel each leading studies that focus respectively on the regulation of transcriptional state, auxin patterning that defines leaf shape or the molecular basis of the PAMP response.

Elsewhere Liam Dolan (Oxford) leads, and Malcolm Bennett (CPIB) is the principal UK contributor on studies that look into different aspects of the key molecular signals in either root hair or lateral root development.

Finally Richard Napier is a co-author on a study that better characterises the molecular basis of the well-used plant growth inhibitor MDCA.

Yang H, Howard M, Dean C (2016) Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC PNAS http://dx.doi.org/10.1073/pnas.1605733113

Dame Caroline Dean and Martin Howard (JIC) lead this follow-on work from a paper highlighted in an ARR from the start of 2016. Here they use the FLOWERING LOCUS C (FLC) locus as a model to study the trans factors that control methylation state. They find a physical interaction between the H3K36 methyltransferase SDG8 (which promotes the active H3K36me3 mark) and the H3K27me3 demethylase ELF6 (which removes the silencing H3K27me3 mark). SDG8 also associated with RNA polymerase II and the PAF1 transcriptional regulatory complex. Therefore the authors suggest that the addition of active histone marks coincides with transcription at the locus whilst SDG8 and ELF6 exhibit co-dependent localisation to FLC chromatin. Therefore this interaction links activation and derepression and coordinates active transcription whilst preventing ectopic silencing.

Abley K, Sauret-Güeto S, Marée AF, Coen E (2016) Formation of polarity convergences underlying shoot outgrowths. Elife. http://dx.doi.org/10.7554/eLife.18165.

Open Access
elife-18165-fig7-v1
Enrico Coen (JIC) is the corresponding author on this investigation that had generated models that predict locations of leaf outgrowth linked to auxin biosynthesis and transport. They use live imaging in wildtype and kanadi1kanadi2 mutants to show that the cellular polarity of the PIN1 auxin transporter is orientated so as to move auxin away from regions with high levels of biosynthesis. In turn, this moves auxin toward regions with high expression of AUX/LAX auxin importers. This data allows the generation of detailed models that describe the processes that control auxin-mediated tissue-patterning (and are impossible to describe in a single paragraph).

Couto D, Niebergall R, Liang X, Bücherl CA, Sklenar J, Macho AP, Ntoukakis V, Derbyshire P, Altenbach D, Maclean D, Robatzek S, Uhrig J, Menke F, Zhou JM, Zipfel C (2016) The Arabidopsis Protein Phosphatase PP2C38 Negatively Regulates the Central Immune Kinase BIK1 PLoS Pathog. http://dx.doi.org/10.1371/journal.ppat.1005811

Open Access

Cyril Zipfel is the lead investigator on this study that links researchers at TSL with colleagues in China and Germany. The focus of this work is the cytoplasmic kinase BIK1, which is a target of several pattern recognition receptors (PRRs) that are involved in the defence response, and the novel protein phosphatase PP2C38, which acts as a negative regulator of BIK1. Under non-inductive conditions PP2C38 prevents BIK1 activity but following pathogen-associated molecular patterns (PAMP) perception, it is phosphorylated and dissociates from BIK1, allowing full activity. This study provides another layer of detail into the complex central immune response that allows plants to response to a vast array of pathogenic microorganisms.

Goh T, Toyokura K, Wells DM, Swarup K, Yamamoto M, Mimura T, Weijers D, Fukaki H, Laplaze L, Bennett MJ, Guyomarc’h S (2016) Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor Development. http://dx.doi.org/10.1242/dev.135319

Open Access

Malcolm Bennett and Darren Wells (CPIB) are authors on this international collaboration that links UK, Japanese, French and Dutch researchers. The essential role of the central organizer center (the quiescent center, QC) is well known in primary root meristem development but its role during lateral root (LR) formation remained unclear. LR formation is characterised by biphasic growth that involves early morphogenesis from the central stele and subsequent LR meristem formation. This study uses 3D imaging to demonstrate that LR QC cells originate from outer cell layers of early primordial, in a SCARECROW (SCR) dependent manner. Perturbing SCR function causes incorrect formation of the LR QC and prevents wildtype LR patterning. The manuscript also contains some excellent videos of growing LRs that are very informative.
AUX1-YFPKim CM, Dolan L (2016) ROOT HAIR DEFECTIVE SIX-LIKE Class I Genes Promote Root Hair Development in the Grass Brachypodium distachyon PLoS Genet.

http://dx.doi.org/10.1371/journal.pgen.1006211 Open Access

This study comes from Liam Dolan’s lab at the University of Oxford and moves their research focus on root hair development from Arabidopsis into the grass Brachypodium distachyon. ROOT HAIR DEFECTIVE SIX-LIKE (RSL) class I basic helix loop helix genes are expressed in cells that develop root hair fate in Arabidopsis and this study indentifies 3 RSl1 genes in Brachypodium which, when ecoptically expressed, are sufficient for the development of root hairs in all cell files. The function of these RSL proteins is conserved as the Brachypodium versions are able to restore a wildtype phenotype to root hair-less Arabidopsis mutants. Even though root hair patterning is significantly different in Brachypodium and Arabidopsis, this study shows the role of the RSL genes is conserved.
RootHairPic
Steenackers WJ, Cesarino I, Klíma P, Quareshy M, Vanholme R, Corneillie S, Kumpf RP, Van de Wouwer D, Ljung K, Goeminne G, Novak O, Zažímalová E, Napier RM, Boerjan WA, Vanholme B (2016) The allelochemical MDCA inhibits lignification and affects auxin homeostasis. Plant Physiology http://dx.doi.org/10.1104/pp.15.01972

Open Access

Richard Napier (Warwick) is the UK PI on this pan-European study that investigates the molecular basis behind the physiological role of the compound phenylpropanoid 3,4-(methylenedioxy)cinnamic acid (MDCA), which inhibits the phenylpropanoid pathway, important in lignin formation. MDCA causes inhibition of primary root growth and increase proliferation of lateral roots, not through lignin perturbation but due to a disruption in auxin homeostasis. MS analysis demonstrates that MDCA causes overall changes in auxin biosynthesis, conjugation and catabolism, similar to changes observed in mutants involved in the phenylpropanoid pathways. These result link auxin and phenylpropanoid biosynthesis pathways and provide a new explanation for the well demonstrated phytotoxic properties of MDCA.

ICAR2016 Meeting Report: Peter Venn

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Published on: August 12, 2016

Almost a thousand researchers attended this year’s international Conference on Arabidopsis research (ICAR) in South Korea. ICAR2016 was my first experience of a large plant science conference, although it wasn’t a completely foreign experience as I recognised a few faces from the 2015 UK PlantSci conference. I was among the hundreds of delegates presenting a poster, and I benefitted greatly from the talks and discussions I had in these sessions. ICAR2016 was a really good opportunity to see what kinds of research are being performed across the world and to discover many novel techniques and developments.

With the two concurrent sessions, almost all of the timeslots contained talks relating to my own interests or the wider interests of the Sorefan lab group. I learnt a lot during the conference, not only new details, but about the high standard of competition in global Arabidopsis research. I also came away with ideas, a potential collaboration and new motivation to get my research published.

Professor Jen Sheen opened the conference with her latest developments in understanding the sugar signalling function of HEXOKINASE1, the glucose receptor that was first identified and characterised by her lab. Amino acids essential for the sugar signalling function of HEXOKINASE1 but not its catalytic function have been identified and are being characterised. This talk was of particular interest to me because my research relates to sugar signalling, and Professor Jen Sheen is the leader of the field. Venn_1

Stem cell development is another of my research areas so it was of interest that a surprising number of talks focussed on cambial development. Professor Hiroo Fukada talked about the role of short peptide ligands and their receptors that regulate xylem formation. Dr Ari Mähönen and Professor Ildoo Hwang talked about different aspects of WOX4 function in cambial development, Whilst Professor Hwang also discussed the role of auxin signalling in cambial development that is mediated through the activity of the BRASSINOSTEROID-INSENSITIVE2-LIKE1 (BIL1) gene.

The meeting also included some excellent research that focussed on shoot apical meristem development. Professor Dave Jackson presented a novel CLAVATA-like peptide that increases floral meristem size and primordia row number in maize and how this peptide was likely linked to the domestication of maize. Professor Naoyuki Uchida presented the role of ERECTA family genes in repressing the cytokinin induction of stem cell maintenance, which is independent of CLV3 signalling.Venn_IMG_0246

However it wasn’t all science as the long days merged into evening sessions of networking at the local bar. This was situated beneath the intriguing K-pop museum where some very talented locals entertained us with karaoke and dancing!

I also used the opportunity to visit several labs in South Korea, including two at Postech in Pohang, and two at Seoul National University. This was a valuable insight into the research culture in South Korea, and an opportunity for further networking. I was really impressed by the scale of some of the research in South Korea as for example, one lab had cloned an entire gene family (of over 70 genes) for a protein-effector interaction screen. I was also able to establish a collaboration with researchers at Seoul National University, inspired by reading a poster from their lab at the conference. I am very grateful to my supervisor, Karim Sorefan and also to the Gatsby Foundation and GARNet for providing the travel grant that enabled me to attend ICAR2016.
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