GARNet Research Roundup: April 27th

This weeks GARNet research roundup features four papers that include Malcolm Bennett (University of Nottingham) as an author. The first three are linked manuscripts that investigate the role of auxin on root hair development that is controlled by varying phosphate levels. Ranjan Swarup provides an audio summary of two of these papers on the GARNet YouTube and podcast feeds.

The fourth paper from Nottingham is a collaboration with GARNet PI Jim Murray (Cardiff University) that characterises the STM gene network and its influence on meristem development.

The fifth paper from the lab of Paul Dupree in Cambridge characterises the stem transcriptome whilst the next paper from Iain Johnston and George Bassel (University of Birmingham) identifies a bet-hedging network that influences seed germination. The final paper features Seth Davies (University of York) as a co-author and investigates the impact of changes in circadian rhythms on short architecture.


Researchers at the University of Nottingham are involved in three back-to-back papers that add a mechanistic framework to the relationship between phosphate and auxin signaling in root hairs.

Bhosale R, Giri J, Pandey BK, Giehl RFH, Hartmann A, Traini R, Truskina J, Leftley N, Hanlon M, Swarup K, Rashed A, Voß U, Alonso J, Stepanova A, Yun J, Ljung K, Brown KM, Lynch JP, Dolan L, Vernoux T, Bishopp A, Wells D, von Wirén N, Bennett MJ, Swarup R (2018) A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate. Nat Commun. 9(1):1409. doi: 10.1038/s41467-018-03851-3

https://www.nature.com/articles/s41467-018-03851-3

Open Access

The first paper is led by Ranjan Swarup and defines components of auxin biosynthetic, transport and signaling pathways that are involved in the change root hair development in response to different phosphate concentrations in Arabidopsis. Ranjan discusses this paper on YouTube.

Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ (2018). Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate. Nat Commun. 9(1):1408. doi: 10.1038/s41467-018-03850-4

https://www.nature.com/articles/s41467-018-03850-4

Open Access

This paper led by Malcolm Bennett uses a rice model to investigate the relationship between auxin and root hair elongation in response to low concentrations of phosphate. They show rice aux1 mutants have significant changes in root architecture.

Dindas J, Scherzer S, Roelfsema MRG, von Meyer K, Müller HM, Al-Rasheid KAS, Palme K, Dietrich P, Becker D, Bennett MJ, Hedrich R (2018) AUX1-mediated root hair auxin influx governs SCF(TIR1/AFB)-type Ca(2+) signaling. Nat Commun. 9(1):1174. doi: 10.1038/s41467-018-03582-5

Open Access

The third paper includes Malcolm Bennett as a co-author and investigates how the auxin transport and signaling pathways stimulate calcium signaling during root hair elongation.


Scofield S, Murison A, Jones A, Fozard J, Aida M, Band LR, Bennett M, Murray JAH (2018) Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network. Development pii: dev.157081. doi: 10.1242/dev.157081

http://dev.biologists.org/content/early/2018/04/12/dev.157081.long

Open Access
GARNet PI Jim Murray is the corresponding author on this manuscript that is led by Dr Simon Scofield and includes collaborators from the University of Nottingham. They have explored the gene regulatory network that is regulated by the key meristem identity gene SHOOT MERISTEMLESS (STM). This network includes an over-representation of transcription factor families, each of which have distinct roles in meristem development. They use in planta experimentation and in silico modeling to investigate the relationship between STM and CUC1 in more detail. Overall this study confirms that STM is a central regulator of shoot meristem function.


Faria-Blanc N, Mortimer JC, Dupree P (2018) A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis. Front Plant Sci. 9:384. doi: 10.3389/fpls.2018.00384

Open Access

Paul Dupree (University of Cambridge) is the corresponding author of this study that uses a range of Arabidopsis cell wall mutants to investigate the stem transcriptome. In plants with defects in xylan synthesis the authors found surprisingly few transcriptional changes. This indicates that once plants have committed to a terminal secondary cell wall program there is little need for transcriptional changes even after cell wall damage.


Johnston IG, Bassel GW (2018) Identification of a bet-hedging network motif generating noise in hormone concentrations and germination propensity in Arabidopsis. J R Soc Interface. 15(141). pii: 20180042. doi: 10.1098/rsif.2018.0042.

Open Access
Iain Johnston (University of Birmingham) leads this study that has identified a bet-hedging network that links hormone signaling during Arabidopsis germination. This type of network allows plants to more easily adapt to varying environmental conditions but can preclude maximum growth. In this system the network is based upon the regulation of ABA synthesis, activity and degradation, which is maintained at a constant mean level even though it exhibits significant noise. They investigate the parameters that might be tweaked to reduce variation in germination rate and therefore might be targets for modification in order to maximise responses under particular environmental conditions.

George Bassel who is a co-author on this paper will be speaking at the GARNet2018 Meeting in York in September.

http://rsif.royalsocietypublishing.org/content/15/141/20180042.long

Rubin MJ, Brock MT, Baker RL, Wilcox S, Anderson K, Davis SJ, Weinig C (2018) Circadian rhythms are associated with shoot architecture in natural settings. New Phytol. doi: 10.1111/nph.15162.

Seth Davies (University of York) is a co-author on this study that assesses the effect of circadian rhythms on aerial phenotypes that lead to fruit production in field grown Arabidopsis. This was assessed over two growing seasons and they show that variation in clock function significantly impacts shoot architecture.

Ranjan Swarup talks to GARNet

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Published on: April 23, 2018

Ranjan Swarup (University of Nottingham) discusses a couple of recent papers published in Nature Communications that describe the relationship between phosphate and auxin signaling in the roots of Arabidopsis and rice plants.

https://www.nature.com/articles/s41467-018-03851-3

https://www.nature.com/articles/s41467-018-03850-4

Arabidopsis Research Roundup: March 9th

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Published on: March 9, 2018

This Arabidopsis Research Roundup has five papers that includes two from the John Innes Centre and two from the University of Edinburgh. Firstly Kristen Bomblies’s group at the JIC have investigated the relationship between temperature and meiotic recombination rates. Secondly Veronica Grieneisen and Stan Maree have developed a mathematical model to characterise cell morphologies taken from a 2D image. Andrew Miller from Edinburgh is a co-corresponding author on a study that shows how the Arabidopsis proteome changes in different photoperiods. In the fourth paper Peter Doerner is a co-author on work that looks at the phosphate starvation response. Finally researchers from Bristol and Nottingham contribute to an investigation into a novel genetic component that controls auxin-induced root hair development.


Lloyd A, Morgan C, Franklin C, Bomblies K (2018) Plasticity of Meiotic Recombination Rates in Response to Temperature in Arabidopsis. Genetics. doi: 10.1534/genetics.117.300588

Open Access

Kristen Bomblies (John Innes Centre) leads this study that investigates the influence of temperature on meiotic recombination rate. They show that in Arabidopsis the number of crossovers positively correlates with increasing temperature. However the mechanistic explanation for the increase at higher temperatures remains opaque as, in contrast to findings from other plants, synaptonemal complex length negatively correlates with temperature.


Sánchez-Corrales YE, Hartley M, van Rooij J, Marée AFM, Grieneisen VA (2018) Morphometrics of complex cell shapes: Lobe Contribution Elliptic Fourier Analysis (LOCO-EFA). Development. doi: 10.1242/dev.15677

http://dev.biologists.org/content/early/2018/02/08/dev.156778.long

Open Access

Veronica Grieneisen and Stan Maree (John Innes Centre) lead this study that has developed the Lobe Contribution Elliptical Fourier Analysis (LOCO-EFA) method. This generates meaningful descriptors from a 2D image of cells that can then be linked to morphological features. This tool allows for the efficient phenotyping of cell morphologies that they demonstrate by analysing images of Arabidopsis leaf pavement cells. They extend this analysis to larger populations where they used LOCO-EFA to predict how cell shapes change when they move into a more crowded space.


Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W (2018) Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. Mol Syst Biol. doi: 10.15252/msb.20177962 Open Access

http://onlinelibrary.wiley.com/doi/10.15252/msb.20177962/abstract

Andrew Miller (University of Edinburgh) is the corresponding author on this collaboration with German and Swiss colleagues that compares the Arabidopsis proteome across four photoperiods. They shows coordinated changes across the proteome, most notably at longer photoperiods in the abundance of proteins involved in photosynthesis and metabolism. They show higher translation rates during the day that correspond with the increased RNA abundance that is a characteristic of circadian rhythms. This ‘translational coincidence’ describes the alignment of higher translation rates with high transcript levels and they assigned a mathematical model in an attempt to explain this phenomenon.


Hanchi M, Thibaud MC, Légeret B, Kuwata K, Pochon N, Beisson F, Cao A, Cuyas L, David P, Doerner P, Ferjani A, Lai F, Li-Beisson Y, Mutterer J, Philibert M, Raghothama KG, Rivasseau C, Secco D, Whelan J, Nussaume L, Javot H (2018) The phosphate fast-responsive genes PECP1 and PPsPase1 affect phosphocholine and phosphoethanolamine content. Plant Physiol. doi: 10.1104/pp.17.01246 Open Access

Peter Doerner (University of Edinburgh) is a co-author on this global study that characterises the phosphate starvation-mediated induction of the HAD-type phosphatases PPsPase1 (AT1G73010) and PECP1 (AT1G17710). They show that expression of these genes closely follows phosphate status but that their activity does not alter phospate content. The role of these proteins is to control phosphocholine and phosphoethanolamine content, which is a output of changing phosphate conditions. The authors conclude that expression of these genes can be an excellent molecular marker for the phosphate starvation response.


www.cell.com/current-biology/fulltext/S0960-9822(18)30083-6

Schoenaers S, Balcerowicz D, Breen G, Hill K, Zdanio M, Mouille G, Holman TJ, Oh J, Wilson MH, Nikonorova N, Vu LD, De Smet I, Swarup R, De Vos WH, Pintelon I, Adriaensen D, Grierson C, Bennett MJ, Vissenberg K (2018) The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Current Biology doi: 10.1016/j.cub.2018.01.050

This Belgian-led study includes contributions from Claire Greirson’s and Malcolm Bennett’s labs in Bristol and Nottingham respectively. They investigate the role of the ERULUS (ERU) protein, an auxin-induced receptor-like kinase, during the development of root hairs. ERU localises to the apical root hair plasma membrane and regulates cell wall composition by altering pectin dynamic. The authors conclude that ERU is a key regulator of auxin-mediated control of root hair development.

Charles Melynk talks to GARNet

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Published on: March 1, 2018

Charles Melnyk discusses a new paper published in PNAS that describes the molecular events that occur during grafting. The paper is entitled ‘Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration

Arabidopsis Research Roundup: February 12th

This weeks Arabidopsis Research Roundup begins with a study from SLCU that investigates the interaction between nitrate and cytokinin signaling in the shoot meristem. Next is research from Sheffield that studies changes to the macromolecular composition of the photosynthetic apparatus following the transition from dark to light. Third are three papers that include University of Edinburgh faculty members as co-authors; Gary Loake is involved in a global study on NO signaling, Karen Halliday is included on a study into the relationship between clock components and the PIF-mediated hypocotyl elongation and Naomi Nakayama contributes to the development of a model that explains PIN protein localisation. Cyril Zipfel (TSL) is a co-author on the fifth paper, which introduces a new signaling component in the defence response and whilst the penultimate paper includes Denis Murphy (University of South Wales) and investigates the effect of dioxins on seed development. The final paper documents research from Manchester and Nottingham that uses a cress endosperm as a model to test the elastic properties of thin biological membranes.


Landrein B, Formosa-Jordan P, Malivert A,, Schuster C, Melnyk CW,, Yang W, Turnbull C, Meyerowitz EM, Locke JCW,, Jönsson H (2018) Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins. PNAS doi: 10.1073/pnas.1718670115.

Open Access

http://www.pnas.org/content/early/2018/01/22/1718670115

Henrik Jonsson and James Locke (SLCU) are corresponding authors on this investigation into the relationship between nitrate and cytokinin signalling in the Arabidopsis shoot meristem (SAM). They show that nitrate availability determines the size of the SAM, which is controlled by the transport of cytokinin precursors from the root to the shoot. A discussion about this paper with lead author Benoit Landrien and Professor Jonsson is available on the GARNet YouTube and iTunes channels.


Wood WHJ, MacGregor-Chatwin C, Barnett SFH, Mayneord GE, Huang X, Hobbs JK, Hunter CN, Johnson MP (2018) Dynamic thylakoid stacking regulates the balance between linear and cyclic photosynthetic electron transfer. Nature Plants. doi: 10.1038/s41477-017-0092-7

Open with this link

This research in this manuscript has come from the University of Sheffield with Matthew Johnson as the corresponding author. They have used atomic force microscopy (AFM) to investigate how the transition from dark to light affects the macromolecular architecture of the photosynthetic apparatus within the thylakoid membrane. This transition does not alter the antenna size of either photosystem yet increases the number of thylakoid grana. Overall these changes serve to regulate the balance between light harvesting, CO2 fixation and enabling the protection of PSII activity from the destructive effects of non-photochemical quenching.


Imran QM, Hussain A, Lee SU, Mun BG, Falak N, Loake GJ, Yun BW (2018) Transcriptome profile of NO-induced Arabidopsis transcription factor genes suggests their putative regulatory role in multiple biological processes. Sci Rep. doi: 10.1038/s41598-017-18850-5.

https://www.nature.com/articles/s41598-017-18850-5

Open Access

Gary Loake (University of Edinburgh) is a contributor to this Korean-led manuscript that has performed expression analysis on plants treated with S-nitrosocysteine (CySNO). They have identified many novel NO-responsive transcription factors and were able to confirm the role of three random TFs in this response following analysis of loss of function mutants. This paper provides new insights into the molecular components that contribute to NO signalling during plant defence and immunity.


Martín G, Rovira A, Veciana N, Soy J, Toledo-Ortiz G, Gommers CMM, Boix M, Henriques R, Minguet EG, Alabadí D, Halliday KJ, Leivar P, Monte E Circadian Waves of Transcriptional Repression Shape PIF-Regulated Photoperiod-Responsive Growth in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2017.12.021

Karen Halliday (University of Ediburgh) is a co-author on this Spanish-led study that investigates how the expression of PHYTOCHROME-INTERACTING FACTORS (PIFs) genes is controlled. The activity of PIFs are responsible for determining the rate of hypocotyl elongation in different light conditions and this paper demonstrates that PSEUDO-RESPONSE REGULATORS PRR9/7/5 proteins act antagonistically to the PIFs by interacting at the promotor of the CDF5 transcription factor. This provides a mechanism to explain the circadian-controlled regulation of hypocotyl cell elongation.


Hernandez V, Barrio RA, Benítez M, Nakayama N, Romero-Arias JR, Villarreal Lujan C (2018) A physico-genetic module for the polarisation of auxin efflux carriers PIN-FORMED (PIN). Phys Biol. doi: 10.1088/1478-3975/aaac99

Naomi Nakayama (University of Edinburgh) is a co-author on this Mexican-led study that proposes a physico-genetic model that explains the localization of PIN auxin transporter proteins to the Arabidopsis plasma membrane. This model confirms experimental observations and allows the prediction that mechanical forces can predominate over molecular components.


www.cell.com/molecular-cell/fulltext/S1097-2765(17)30983-8

Wang J, Grubb LE, Wang J, Liang X, Li L, Gao C, Ma M, Feng F, Li M, Li L, Zhang X, Yu F, Xie Q, Chen S, Zipfel C, Monaghan J, Zhou JM (2018) A Regulatory Module Controlling Homeostasis of a Plant Immune Kinase. Mol Cell. doi: 10.1016/j.molcel.2017.12.026

This Chinese-led paper includes Cyril Zipfel (TSL) as a co-author and identifies the U-box proteins PUB25 and PUB26 as E3 ligases for the cytoplasmic kinase BIK1, which is a key rate limiting component of the plant defence response. This multi-protein regulatory module provides another level of complexity to our understanding of the molecular factors involved in plant immunity.


Hanano A, Almousally I, Shaban M, Murphy DJ (2018) Exposure of Arabidopsis Plants to Dioxin Results in a Wrinkled Seed Phenotype that is likely due to 20S Proteasomal Degradation of WRI1. J Exp Bot. doi: 10.1093/jxb/ery027

Denis Murphy (University of South Wales) is a co-author on this Syrian-led study that uses Arabidopsis seeds to test the negative effects of dioxins. Seeds treated with dioxins have a wrinked phenotype that corresponds to changes in the expression of genes related to lipid and carbohydrate metabolism. Overall this study reveals a novel set of genetic changes effects caused by dioxins that explain the profound effects on seed development.


S. P. Pearce, J. R. King, T. Steinbrecher, G. Leubner-Metzger, N. M. Everitt, M. J. Holdsworth (2018) Finite indentation of highly curved elastic shells Proceedings of the Royal Society A doi: 10.1098/rspa.2017.0482

Open Access

Plant scientist Mike Holdsworth (University of Nottingham) is a co-author on this paper that has used the endosperm from garden cress (Lepidium sativum) as the experimental model to define the elastic properties of a thin biological surface. Indentation experiments have been classically used to measure these properties and then develop mathematically models that explain their characteristics. These models rely on an assumed flat surface whereas in reality any surface will often be curved. By obtaining measurements from identations studies on the cress endosperm they are able to better refine the models that explain the properties of the membrane in this context.

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.
https://garnet-ge-workshop.weebly.com/registration.html

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:
https://garnet-ge-workshop.weebly.com/accomodation-and-transport.html

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.

https://www.nature.com/articles/nchembio.2555
https://www.nature.com/articles/nchembio.2555

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!!!

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