Arabidopsis Research Roundup: December 8th.

This weeks Research Roundup begins with two papers from the University of Edinburgh on very different topics of Arabidopsis research. Firstly Alistair McCormick and Sofirtios Tsaftaris introduce a new low-cost phenotyping platform whilst Gerben Ooijen’s group has analysed the role of SUMOylation in the control of the circadian clock. The next three papers each involve wide UK collaborations and either look at plant nutrient composition (Nottingham, Dundee, York), the role of N-end rule pathway in the control of seed storage mobilisation (Rothamsted, Nottingham, Oxford, Birmingham, Cambridge) or the development of a new tool for the study of phloem sieve elements (Leeds, Rothamsted, Cambridge, Newcastle). The penultimate paper from Daniel Zilbermann (JIC) highlights the global mechanisms of methyltransferase function in Arabidopsis and mice whilst the final paper from Alexandre Ruban (QMUL) and co-authors continues his groups work to unpick the specifics of NPQ.


Dobrescu A, Scorza LCT, Tsaftaris SA, McCormick AJ (2017) A “Do-It-Yourself” phenotyping system: measuring growth and morphology throughout the diel cycle in rosette shaped plants. Plant Methods. doi: 10.1186/s13007-017-0247-6

Open Access

University of Edinburgh colleagues Alistair McCormick and Sofirtios Tsaftaris lead this work that presents a low cost phenotyping system for the analysis of the growth rate and phenotypic characteristics of Arabidopsis thaliana rosettes. The software that they have developed allows the accurate segmentation of multiple rosettes within a single image and overall offers a straightforward solution for automated phenotyping across a range of growth environments.


Hansen LL, van den Burg HA, van Ooijen G (2017) Sumoylation Contributes to Timekeeping and Temperature Compensation of the Plant Circadian Clock. J Biol Rhythms. doi: 10.1177/0748730417737633

Gerben van Ooijen (University of Edinburgh) is the corresponding author of this work that has identified SUMOylation as a novel mechanism of regulating circadian clock genes in Arabidopsis. Plants with defects in sumoylation have altered circadian periods that exhibit incorrect temperature compensation. Overall these results indicate that sumoylation importantly buffers clock function in response to changing temperatures.


Alcock TD, Havlickova L, He Z, Bancroft I, White PJ, Broadley MR, Graham NS (2017) Identification of Candidate Genes for Calcium and Magnesium Accumulation in Brassica napus L. by Association Genetics. Front Plant Sci. doi: 10.3389/fpls.2017.01968

Open Access

Neil Graham and Martin Broadley (University of Nottingham) are the corresponding authors of this study that has taken advantage of the Brassica napus Associative Transcriptomes RIPR diversity panel developed by Ian Bancroft’s lab in York. Novel loci involved with an altered response to calcium and magnesium were identified in B.napus before mineral composition was analysed in Arabidopsis mutants defective in orthologous genes. The analysed plants exhibited alteration in mineral composition, meaning that the associated Brassica loci might be targets for future breeding strategies aimed at improving plant nutrient compositions.


Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL (2017) N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. New Phytol. doi: 10.1111/nph.14909

Freddie Theodoulou (Rothamsted Research) is the corresponding author of this research that involved a collaboration with colleagues in Cambridge, Birmingham, Nottingham and Oxford. They have performed a proteomic analysis on etiolated seedlings to identify those proteins designated for degradation by the N-end rule pathway. They analysed prt6 mutant plants that lack the function of the E3 ligase PROTEOLYSIS6 (PRT6) and discovered that N-terminal peptides from 45 protein groups were upregulated in this mutant, corresponding to the equivalent downregulation of several known N-end rule proteases. Overall the authors show that PRT6 plays an important role in the regulation of seed storage mobilisation in young seedlings and is therefore a possible future target to manipulate the plant responses to adverse environmental conditions. Dr Kirsty Hassall, a statistician at Rothamsted, is an author on this paper and in the latest edition of the GARNish newsletter explains how she interacts with plant scientists during her work.


Torode TA, O’Neill RE, Marcus SE, Cornuault V, Pose-Albacete S, Lauder RP, Kracun SK, Gro Rydahl M, Andersen MCF, Willats WGT, Braybrook SA, Townsend BJ, Clausen MH, Knox JP (2017) Branched pectic galactan in phloem-sieve-element cell walls: implications for cell mechanics. Plant Physiol. doi: 10.1104/pp.17.01568 Open Access

Paul Knox (University of Leeds) is the corresponding author of this study that includes contributions from researchers at SLCU, Newcastle and Rothamsted. This work is based around the development of a monoclonal antibody, LM26 that is able to recognize a β-1,6-galactosyl substitution of β-1,4-galactan. LM26 has allowed the identification of this unusual branched galactan that is specific to phloem elements and the authors hope that it can be a useful tool in future studies on the biology of phloem elements


Lyons DB, Zilberman D (2017) DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. Elife. doi: 10.7554/eLife.30674 Open Access

Daniel Zilberman has recently moved to the John Innes Centre and is the lead author of this work that was conducted when he was working in US. This research is a cross-kingdom analysis showing that nucleosome-free DNA is the preferred target for methyltransferases in both Arabidopsis and mice, and that nucleosomes appear to be a barrier to the function of these enzymes. Furthermore they demonstrate that linker-specific methylation that is usually absent in Arabidopsis can be introduced by removal of histone H1. This shows that flowering plants still possess this ability despite its loss, during the evolution of H1, over a billion years ago.


Tutkus M, Chmeliov J, Rutkauskas D, Ruban AV, Valkunas L (2017) Influence of the Carotenoid Composition on the Conformational Dynamics of Photosynthetic Light-Harvesting Complexes. J Phys Chem Lett. doi: 10.1021/acs.jpclett.7b02634

Alexandre Ruban (QMUL) is a co-author on this study that investigates the role that carotenoid composition plays in the control of Non-photochemical quenching (NPQ), a mechanism that protects the photosynthetic apparatus from light-damage. Arabidopsis mutants with differing carotenoid compositions were analysed for the dynamics of the conformation switches that occur during NPQ. Interestingly they show that LHCII has robust function  that is resistant to different carotenoid concentrations.

Arabidopsis Research Roundup: Nov 24th

The week’s UK Arabidopsis research roundup includes seven papers from groups who work on a range of topics.

Firstly Antony Dodd (Bristol) investigates the role of sugar signaling during hypocotyl elongation and provides an audio description of this groups work. Secondly Mike Holdsworth (Nottingham) leads a paper that demonstrates the importance of the N-rule pathway in the response to abiotic stresses. Thirdly are a set of papers that have developed models on three different topics. Mike Blatt’s group at Glasgow University has a cross-scale model that is applied to stomatal opening whilst Stan Maree and Veronica Griensien (JIC) use modeling to predict how the topology of pavement cells is determined. Finally Arabidopsis is used as an example that fits a model that investigates how critical mutation rate (CMR) changes with population size. In the sixth paper Lorraine Williams and colleagues (University of Southampton) investigate the function of a rice transport protein involved in manganese tolerance by expressing it in Arabidopsis. The final paper from Jerzy Paszkowski (SLCU) outlines a novel screening strategy for retrotransposons and the identification of an ecotype specific element.


Simon NM, Kusakina J, Fernández-López Á, Chembath A, Belbin FE, Dodd AN (2017) The energy-signalling hub SnRK1 is important for sucrose-induced hypocotyl elongation. Plant Physiol. doi: 10.1104/pp.17.01395

Open Access

This UK-wide collaboration is led by Anthony Dodd at the University of Bristol and has looked at the factors that control hypocotyl elongation in response to sugar signalling. This response is integrated through the sugar-signalling hub, SnRK1 and is regulated by trehalose-6-phosphate (Tre6P). They also integrate hormone signalling and the influence of diurnal rhythms into the control of this process, importantly showing that the ubiquitous sugar regulator hexokinase is not involved in this process.

Antony kindly provides an audio description of this research that can be found on YouTube or on the GARNet iTunes channel. Please subscribe!


Vicente J, Mendiondo GM, Movahedi M, Peirats-Llobet M, Juan YT, Shen YY, Dambire C, Smart K, Rodriguez PL, Charng YY, Gray JE, Holdsworth MJ (2017) The Cys-Arg/N-End Rule Pathway Is a General Sensor of Abiotic Stress in Flowering Plants. Current Biology doi: 10.1016/j.cub.2017.09.006

Open Access

Mike Holdsworth (University of Nottingham) is the corresponding author of this collaboration with colleagues from Sheffield, Spain and Taiwan that investigates how the N-rule degradation pathway acts a sensor of general abiotic stress in both Arabidopsis and Barley. These responses are integrated through degradation of the group VII Ethylene Response Factor transcription factors (ERFVIIs) family via direct and indirect pathways. In addition they link ERFVII activity with chromatin-remodeling ATPase BRAHMA providing evidence for a single mechanism that links the responses to a number of environmental signals.


Wang Y, Hills A, Vialet-Chabrand SR, Papanatsiou M, Griffiths H, Rogers S, Lawson T, Lew V, Blatt MR (2017) Unexpected Connections between Humidity and Ion Transport Discovered using a Model to Bridge Guard Cell-to-Leaf Scales. Plant Cell. doi: 10.1105/tpc.17.00694

Open Access

Mike Blatt (University of Glasgow) leads this collaboration with researchers at the Universities of Cambridge and Essex. They have developed the OnGuard2 quantitative systems platform that integrates numerous parameters that control guard cell dynamics across many scales including at molecular, cellular, tissue and canopy levels. They experimentally demonstrate that OnGuard2 faithfully reproduces the kinetics of real stomatal movement and therefore that this modeling is able to bridge the micro-macro divide.


Carter R, Sánchez-Corrales YE, Hartley M, Grieneisen VA, Marée AFM (2017) Pavement cells and the topology puzzle. Development. doi: 10.1242/dev.157073

Stan Maree and Veronica Griensien (John Innes Centre) lead this study that has looked at the patterning of 50000 Arabidopsis pavement cells to understand the topological signatures that exist in this population. They have developed a heuristic cellular division rule to produce a model that can reproduce their observations by predicting how these cells divide. They confirmed their model by tracking 800 mitotic events, allowing them to conclude that distinct topology is not a direct consequence of the jigsaw-like shape of the cells, but rather owes itself to life-history-driven process, with limited impact from cell surface mechanics.


Aston E, Channon A, Belavkin RV, Gifford DR, Krašovec R, Knight CG (2017) Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover. Sci Rep. doi: 10.1038/s41598-017-14628-x

Open Access

In this study a team of computational biologists from Keele, Middlesex and Manchester have used Arabidopsis as an exemplar to understand how critical mutation rate (CMR) provides insights into the shift between survival-of-the-fittest and survival of individuals with greater mutational robustness. They have produced a simulation for these parameters that predicts outcomes for a range of biological organisms, showing that CMR decreases with reduced population size. They suggest that the model can be used to understand the conservation strategies exhibited in populations that are approaching extinction.


Farthing EC, Menguer PK, Fett JP, Williams LE (2017) OsMTP11 is localised at the Golgi and contributes to Mn tolerance. Sci Rep. doi: 10.1038/s41598-017-15324-6
Lorraine Williams (University of Southampton) and her colleagues have identified a transporter protein from rice, OsMTP11 that is involved in mangenase tolerance. They show that heterologous expression of this protein is able to rescue the manganese sensitive phenotype of Arabidopsis mtp11-3 knockouts. They show that OsMTP11 localises to the Golgi and have also conducted site directed mutagenesis to identify key residues that are important for the function of this protein.


Griffiths J, Catoni M, Iwasaki M, Paszkowski J (2017) Sequence-independent identification of active LTR retrotransposons in Arabidopsis. Mol Plant. doi: 10.1016/j.molp.2017.10.012

Open Access

Jerzy Paszkowski (SLCU) leads this single-figure short manuscript that has characterised the population of retrotransposons in Arabidopsis. They develop a novel cost-effective screening strategy that allows them to identify sequences found on extrachromosomal DNA (ecDNA), which includes a retroelement found in Lansberg erecta but not in the reference genome ecotype Col-0.

Arabidopsis Research Roundup: October 23rd

Different aspects of plant cell wall biology dominant the first few papers of this weeks Arabidopsis Research Roundup. Firstly Andrew Fleming (University of Sheffield) and colleagues identify that a specific type of cell wall stiffening is important in control of stomatal opening. Secondly are two papers from the lab of Paul Dupree (University of Cambridge) that investigate the role that xylan modifications play in the formation of the cell wall. Finally in this broad area John Runions (Oxford Brookes) and colleagues show that attachment to the cell wall is critical for correct function of the dynamic actin filament network. Elsewhere Jerry Roberts (CPIB) leads a study that looks at proteins that control floral development. Next the group of Alexander Jones  at SLCU has developed an exciting new tool that allows for in vivo visualization of the plant hormone GA. Finally the lab of Phil Wigge (also at SLCU) further expands their work that dissects the signaling pathways that controlling the response to temperature.


Carter R, Woolfenden H, Baillie A, Amsbury S, Carroll S, Healicon E, Sovatzoglou S, Braybrook S, Gray JE, Hobbs J, Morris RJ, Fleming AJ (2017) Stomatal Opening Involves Polar, Not Radial, Stiffening Of Guard Cells. Curr Biol. doi: 10.1016/j.cub.2017.08.006 Open Access

This broad UK collaboration is led by Andrew Fleming at the University of Sheffield and looks into the factors that control stiffening of cell walls in stomatal guard cells. They use Atomic Force Microscopy to show that stiffening of the polar regions of guard cell walls pins down these ends of cells during stomatal opening. This study provides exciting new insights into the importance of cell wall dynamics on stomatal opening and likely has significant agronomic importance.


Grantham NJ, Wurman-Rodrich J, Terrett OM, Lyczakowski JJ, Stott K, Iuga D, Simmons TJ, Durand-Tardif M, Brown SP, Dupree R, Busse-Wicher M, Dupree P (2017) An even pattern of xylan substitution is critical for interaction with cellulose in plant cell walls. Nat Plants doi: 10.1038/s41477-017-0030-8

Lyczakowski JJ,,, Wicher KB,, Terrett OM, Faria-Blanc N, Yu X, Brown D,, Krogh KBRM, Dupree P,,, Busse-Wicher M (2017) Removal of glucuronic acid from xylan is a strategy to improve the conversion of plant biomass to sugars for bioenergy. Biotechnol Biofuels. doi: 10.1186/s13068-017-0902-1

Open Access

Paul Dupree (University of Cambridge) is involved in two papers that investigate the chemical decorations that adorn components of the plant cell wall. In the first paper they demonstrate that the incorrect addition of acetyl esters onto xylan prevents the formation of the secondary cell wall due to a reduced interaction between xylan and cellulose microfibrils. They undertake a genetic study to show that the ESKIMO1/XOAT1/TBL29, a xylan-specific O-acetyltransferase is responsive for correct attachment of acetyl esters to xylan.

In the second paper they show that a reduction in the attachment of the acetyl ester glucuronic acid to xylan allows increased isolation of ethanol following saccharification. This has enormous potential significance in ongoing attempts to generate lignocellulose biomass that is more amenable to conversion into potential biofuels.


Tolmie F, Poulet A, McKenna J, Sassmann S, Graumann K, Deeks M, Runions J (2017) The cell wall of Arabidopsis thaliana influences actin network dynamics. J Exp Bot. doi: 10.1093/jxb/erx269.
This collaboration between Oxford Brookes and Exeter Universities looks in details at the Arabidopsis actin filament network using a set of novel imaging tools. In addition they show that the network is distributed when the link to the cell wall is disrupted. As might be expected this also effects the function of the network as evidenced by changes in Golgi body motility.


González-Carranza ZH, Zhang X, Peters JL, Boltz V, Szecsi J, Bendahmane M, Roberts JA (2017) HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression. PLoS One.

doi: 10.1371/journal.pone.0185106 Open Access

Jerry Roberts (CPIB, Nottingham) leads a collaboration with Dutch and French colleagues to investigate the role of the F-box gene HAWAIIAN SKIRT in control of flower development. This protein acts by interacting with the CUC-SHAPED COTYLEDON 1 (CUC1) and CUC2 transcription factors to restrict petal size by altering cell proliferation and mitotic growth.


Rizza A, Walia A, Lanquar V, Frommer WB, Jones AM (2017) In vivo gibberellin gradients visualized in rapidly elongating tissues. Nat Plants. doi: 10.1038/s41477-017-0021-9

Free with the link: rdcu.be/wnOh

Alexander Jones (SLCU) collaborates with Wolf Frommers’ lab in Stanford to develop a novel tool to analyse the plant hormone gibberellin in planta. This optogenetic biosensor protein allowed them to show that GA levels correlate with cell length in hypocotyl and root tissues. GA levels are dependent on PIF signalling in a relationship that controls rapid tissue elongation in reponse to favourable environmental conditions. We’re pleased to announce that Alexander will be speaking at next September’s GARNet2018: A Plant Science Showcase at the University of York.


Cortijo S, Charoensawan V, Brestovitsky A, Buning R, Ravarani C, Rhodes D, van Noort J, Jaeger KE, Wigge PA (2017) Transcriptional regulation of the ambient temperature response by H2A.Z-nucleosomes and HSF1 transcription factors in Arabidopsis. Molecular Plant doi: 10.1016/j.molp.2017.08.014

Open Access

Phil Wigge (SLCU) leads this work that investigates how the temperature responsive histone variant H2A.Z interacts with heat shock transcription factors (HSFs). They find that the activity of HSFs is able to evict H2A.Z histones yet at non-inducible temperatures these heat responsive genes show an over-representation of H2A.Z-nucleosomes. They demonstrate that this relationship allows plants to be primed to rapidly response to temperature change whilst preventing leaky transcription in times of low temperature.

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.

Arabidopsis Research Roundup: July 19th

There are six papers in this weeks Arabidopsis Research Roundup. Two of these include research on the stomatal patterning gene TMM. Firstly a White Rose consortium investigates the ancestral basis of stomatal patterning, whilst a Glasgow-based study investigates the relationship between patterning and the dynamics of guard cell opening. The GARNet committee is represented by work from Cardiff that looks at the relationship between seed size and shoot branching and also from Cambridge in research that studies meiotic recombination in genomic regions important for pathogen defense. Finally are two studies that look into aspects of root and shoot patterning and include co-authors from CPIB in Nottingham or the John Innes Centre.

Caine R, Chater CC, Kamisugi Y, Cuming AC, Beerling DJ, Gray JE, Fleming AJ (2016) An ancestral stomatal patterning module revealed in the non-vascular land plant Physcomitrella patens Development

http://dx.doi.org/10.1242/dev.135038 Open Access

This study is a collaboration between labs in Sheffield and Leeds, led by Andrew Fleming (Sheffield). They investigate the role that the signalling module comprised of Epidermal Patterning Factors (EPFs), ERECTA and TMM play during the evolution of stomatal patterning. This module is known to play an important role in Arabidopsis and in this study the authors show that the moss Physcomitrella patens contains homologs of each of the genes and that they perform the same function. When P.paten versions of these genes are transferred to equivalent Arabidopsis mutants they show conserved function demonstrating that this module is an example of an ancestral patterning system.

Andrew Fleming provides a brief audio description of this manuscript:

Papanatsiou M, Amtmann A, Blatt MR (2016) Stomatal spacing facilitates guard cell ion transport independent of the epidermal solute reservoir. Plant Physiol. http://dx.doi.org/10.1104/pp.16.00850 Open Access

Mike Blatt and Anna Amtmann (University of Glasgow) are the co-supervisors for this study into the relationshop between ion transport in stomatal guard cells and their physical positioning within a leaf. They used a genetic approach to assess the effect of stomatal clustering, showing that too many mouths (tmm) mutant plants have reduced stomatal movements associated with alterations in K+ channel gating and coincident with a surprising reduction in the level of K+ ions in guard cells. These results underline the importance of stomatal spacing in this process but do not provide a full explanation into the alteration in K+ ion dynamics.

Sornay E, Dewitte W, Murray JAH (2016) Seed size plasticity in response to embryonic lethality conferred by ectopic CYCD activation is dependent on plant architecture Plant Signaling and Behaviour e1192741

http://dx.doi.org/10.1080/15592324.2016.1192741 Open Access

From http://dx.doi.org/10.1080/15592324.2016.1192741
From http://dx.doi.org/10.1080/15592324.2016.1192741

This research comes from the lab of GARNet PI Jim Murray (Cardiff) and investigates cell proliferation and growth within a developing seed. They previously have shown that targeting of D-type cyclin CYCD7;1 to the central cell and early endosperm can trigger nuclear divisions and ovule abortion, which leads to a smaller number of larger seed. In this study they show that development of larger seed in transgenic plants is influenced by the architecture of the mother, as plants with increased side branches, caused by pruning of the main stem, do not generate this phenotype. This is indicative of a close relationship between the amount of resources allocated to different parts of the plant and that a transgenic effect was altered by a different plant morphology. This should provide an important insight into future work that aims to define the effect of any particular transgenic alteration.

Choi K, Reinhard C, Serra H, Ziolkowski PA,, Underwood CJ,, Zhao X, Hardcastle TJ, Yelina NE, Griffin C, Jackson M, Mézard C, McVean G, Copenhaver GP,, Henderson IR (2016) Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLoS Genet. 12(7):e1006179.

http://dx.doi.org/10.1371/journal.pgen.1006179 Open Access

GARNet advisory board member Ian Henderson (Cambridge) is the corresponding author of this study that involves contributions from the UK, US, Poland and France. They investigate genomic regions that show increased meiotic recombination, which is predicted to occur coincident with genes involved in pathogen defence given their requirement to adapt to new external challenges. This study focuses on NBS-LRR domain proteins that tend to physically cluster in the Arabidopsis genome. Interesting they discovered both hot and coldspots for meiotic recombination that associate with NBS-LRR clusters, the later often correlating with structural heterozygosity. In a more detailed dissection of 1000 crossovers in the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R hotspot, they discovered higher recombination frequencies associating with known sequence motifs important for the pathogen response, which were influenced by ecotype-specific factors. Ultimately the authors note that there is a complex relationship between regions of meiotic recombination, structural heterozygosity and the evolutionary pressures that occurs with host-pathogen relationships.

Orman-Ligeza B, Parizot B, de Rycke R, Fernandez A, Himschoot E, Van Breusegem F, Bennett MJ, Périlleux C, Beeckman T, Draye X (2016) RBOH-mediated ROS production facilitates lateral root emergence in Arabidopsis. Development http://dx.doi.org/10.1242/dev.136465 Open Access

From http://dx.doi.org/10.1242/dev.136465
From http://dx.doi.org/10.1242/dev.136465

 Malcolm Bennett (CPIB) is the sole UK-based co-author on this study led by Belgian collaborators and investigates the role of reactive oxygen species (ROS) in auxin-regulated lateral root (LR) formation. They show that ROS can reactivate LR primordia and pre-branch sites, resulting in increased LR numbers. This occurs in both wildtype and in auxin mutants that have reduced numbers due to changes in auxin-mediated cell wall remodeling. ROS is deposited in the apoplast of emerging LR cells in a pattern that is coincident with the expression of the RESPIRATORY BURST OXIDASE HOMOLOGS (RBOH) genes. Concomitantly the altered expression of RBOH was shown to affect the development and emergence of LRs. This adds a further level of complexity to the current understanding of the signaling factors that converge to facilitate LR growth.

 

Shi B,, Zhang C, Tian C, Wang J,, Wang Q,, Xu T,, Xu Y, Ohno C, Sablowski R, Heisler MG, Theres K, Wang Y, Jiao Y (2016) Two-Step Regulation of a Meristematic Cell Population Acting in Shoot Branching in Arabidopsis. PLoS Genet. http://dx.doi.org/10.1371/journal.pgen.1006168 Open Access

This Chinese-led study includes Robert Sablowski (JIC) as a co-author and studies the factors that influence the development of axillary meristems. They use innovative live imaging to show that SHOOT MERISTEMLESS (STM) is continuously expressed and that this dependent on a leaf axil auxin minimum. Once STM expression is lost then the axil is unable to form a meristem even if STM is switched back later in development, indicating that cells undergo an irreversible developmental commitment. The expression domain of STM is under cell-type specific control of REVOLUTA (REV) DNA binding. Overall this study demonstrates that meristematic competence and initiation is dependent on differing levels of the key regulator STM.

From http://dx.doi.org/10.1371/journal.pgen.1006168
From http://dx.doi.org/10.1371/journal.pgen.1006168

Brassica Research Report: 2015

The Arabidopsis Research Roundup has been put to bed for 2015 so in the leadup to the Christmas we’ll take a look at some of the papers that have been published in 2015 by UK researchers working ondifferent plants.
Today we focus on Brassica species and by looking at papers from throughout 2015 this selection touches on a broad selection of research areas. Chronologically first is a study from Nottingham University that looks at the ability of Brassica rapa to take up specific elements, such as Zn, Ca and Mg. Secondly is a study that documents the parameters that make different cultivars of Brassica napus useful in biorefining. Thirdly we highlight where Brassica oleracea has been used both in preference to, and alongside Arabidopsis in a study that investigates meiotic recombination. Next is a study that investigates the relationship between leaf colour and insect herbivory. Finally we highlight a recent publication from the John Innes Centre that demonstrates the ability to generate gene-edited B.oleracea.
The varieties of Brassica
March

Blasco B, Graham NS, Broadley MR (2015) Antioxidant response and carboxylate metabolism in Brassica rapa exposed to different external Zn, Ca, and Mg supply.
J Plant Physiol. 176:16-24 http://dx.doi.org/10.1016/j.jplph.2014.07.029
Martin Broadley and Neil Graham from Nottingham University lead this study that investigates antioxidant response and carboxylate metabolism in Brassica rapa. The authors looked at these parameters in the presence of varying amounts of zinc, calcium or magnesium in experiments that aimed to simulate the response to deficiency or toxicity of these elements. Plants grown with high concentrations of these elements showed increased shoot biomass, hydrogen peroxide, total ascorbate and increasing activity of enzymes involved in removal of antioxidants. This indicates that B.rapa is particularly sensitive to high levels of these elements. The information provided in this study represents important baseline measurements that will aid the future characterisation of B.rapa TILLING lines, generated by the RevGenUK service at the JIC.

July

Wood IP, Wellner N, Elliston A, Wilson DR, Bancroft I, Waldron KW (2015) Effect of Brassica napus cultivar on cellulosic ethanol yield. Biotechnol Biofuels. 8:99. http://dx.doi.org/10.1186/s13068-015-0278-z Open Access
Keith Waldron (Institute of Food Research, JIC) leads this collaboration with the University of York that investigates how the sugar composition of Brassica napus alters its ability to be used as a source for biorefining. They found significant differences in the saccharification and fermentation yields after the processing of straw obtained from 17 different B.napus cultivars. Surprisingly glucan-rich straw was not correlated with higher saccharification or ethanol yields but rather the non-cellulosic components were more reliable indicators of substrate quality, with the amount of pectins and arabinogalactans having the greatest impact on saccharification. Ultimately this study finds that pectin concentration is most likely to determine to effectiveness of the cultivar in the production of bioethanol. This is important information for the future development of different dicot species for use in this aspect of biorefining.

July

Lambing C, Osman K, Nuntasoontorn K, West A, Higgins JD, Copenhaver GP, Yang J, Armstrong SJ, Mechtler K, Roitinger E, Franklin FC (2015) Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers PLoS Genetics 11(7):e1005372 http://dx.doi.org/10.1371/journal.pgen.1005372 Open Access

Immunolocalisation of proteins during meiotic recombination in Brassica.
Immunolocalisation of proteins during meiotic recombination in Brassica.

Chris Franklin (Birmingham) is the leader on the UK-US-Austrian collaboration that looks at the role of the PCH2 protein during meiotic recombination. Although much of this study uses Arabidopsis mutant plants, the initial immunoprecipitations that led to identification of novel factors were performed using pollen mother cells from Brassica oleracea. Subsequently some important imaging also takes place in B.oleracea. The authors use structured illumination microscopy (SIM) to investigation the localisation of synaptonemal complex formation during meiosis and the close relationship between Arabidopsis and B.oleracea allowed the authors to use to same reagents fo these experiments. This paper was featured in an Arabidopis Research Roundup earlier in the year.

September.

Green JP, Foster R, Wilkins L, Osorio D, Hartley SE (2015) Leaf Colour as a Signal of Chemical Defence to Insect Herbivores in Wild Cabbage (Brassica oleracea). PLoS One 10(9):e0136884 http://dx.doi.org/10.1371/journal.pone.0136884 Open Access

This collaboration between York and Sussex Universitites is led by Sue Hartley and Daniel Osorio and look into the role that leaf colour plays in the defence response in wild cabbage. This aspect of plant physiology has been proposed as being important in defence against insect herbivory but this is the first instance where real data from wild populations has been obtained on this topic. The authors found that variation in leaf colour and brightness corresponded to particular glucosinolate levels as well as of the ability of certain herbivores to colonise the leaves. As might be predicted, leaves with lower levels of glucosinolate coincided with faster growth rates of lepidopteran larvae. However in a controlled experiment neither adult butterflies or adult aphids showed a preference for leaves of different colours. This therefore might suggest that although in the field herbivores may benefit from colonising leaves with lower defence chemicals (and an altered colour), the adults do not have the ability to select for these particular leaves, indicating that selection of leaves is either down to chance or other uninvestigated parameters.

November.

Lawrenson T, Shorinola O, Stacey N, Li C, Østergaard L, Patron N, Uauy C, Harwood W (2015) Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease Genome Biol. 16:258. http://dx.doi.org/10.1186/s13059-015-0826-7 Open Access

An example of successfully gene edited Brassica. From Genome Biology
An example of successfully gene edited Brassica. From Genome Biology

This is a collaboration between Wendy Harwood, Cristobal Uauy, Nicola Patron and Lars Ostargaard from the John Innes Centre and the Sainsbury Lab in Norwich. Over the past few years, CRISPR-Cas technology has been presented as important technology to be used in the future generation of gene edited crops. However only a few studies have been published to date where this technology has been effectively used. This paper describes the use of CRISPR-Cas to generate specific mutations in both barley and Brassica oleracea. Across both species they identified targeted mutations in 10%-25% of the first generation plants although interestingly they were also able to identify B.oleracea mutants in the T0 generation. They also observed off-target activity in both species even though the designed guide RNAs contains mismatches with the incorrectly edited sequences.
This is important work demonstrating that this type of gene editing can be used to rapidly generate stable mutants in crop species. The creation of mutants in off-target genes is a potential concern from a regulatory perspective although can be viewed as a positive factor for targeting multigene families that do not have appropriate identical target sequences.

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