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.
Venn_2

Arabidopsis Research Roundup: August 8th

This weeks Arabidopsis Roundup contains a wide breadth of UK research. Firstly the lab of Jurriaan Ton undertakes a global analysis into the role of methylation in the immune response. Jurriaan kindly provides a short audio description of this work. Secondly Dame Caroline Dean’s lab further add to our understanding of the vernalisation response in Arabidopsis. Thirdly is work from Rothamstead that evaluates the fatty acid composition of the seed aleurone while fourthly is a study from Durham and Oxford Brookes that introduces a novel regulator of autophagy. Finally is a study that adds clarity to the phenotypic effects resulting from ascorbic acid deficiency.

López Sánchez A, H M Stassen J, Furci L, Smith LM, Ton J (2016) The role of DNA (de)methylation in immune responsiveness of Arabidopsis Plant Journal http://dx.doi.org/10.1111/tpj.13252 Open Access

Jurriaan Ton is the corresponding for study from the University of Sheffield that looks into the role of reversible methylation on the Arabidopsis immune response. Methylation is a well known regulator of gene expression and in this research the authors attempt to interrogate its effect on the immune response. Hypo-methylated mutants are more resistant, whilst hyper-methylated mutants are more suspectible to the biotrophic pathogen Hyaloperonospora arabidopsidis (Hpa). Downstream gene expression changes in these methylation mutants focus at the level of cell-wall modification and salicylic acid (SA)-responses. Oppositely the hypo-methylated mutant nrpe1 is more suspective to the necrotrophic pathogen Plectosphaerella cucumerina whilst the hyper-methylated ros1 mutant is resistant to this organism. The Ton-lab has been involved in the discovery of the exciting phenomon of transgenerational acquired resistance, and both nrpe1 and ros1 fail to develop this response against Hpa. Global gene expression shows that either NRPE1 or ROS1 influence about 50% of the gene expression changes that occur following Hpa infection. Finally since less than 15% of genes with altered gene expression reside close to NRPE1 or ROS1, the authors are able to propose that much of this regulation is due to methylation effects that act in trans- throughout the genome.

Jurriaan kindly provides a comprehensive description of this work:


Qüesta JI, Song J, Geraldo N, An H, Dean C (2016) Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization Science. 353(6298):485-8 http://dx.doi.org/10.1126/science.aaf7354

VAL_pic
From http://science.sciencemag.org/content/353/6298/485

Dame Caroline Dean (John Innes Centre) is the lead author of this manuscript that builds upon the portfolio of work from her lab aimed at characterising the vernalization response. This work again uses the FLOWERING LOCUS C (FLC) gene as a model to study the factors that allow gene-silencing mediated by Polycomb silencing complexes. The authors find that a single intragenic point mutation prevents nucleation of the homeodomain-Polycomb repressive complex 2 (PHD-PRC2) to this region, a process that involves the transcriptional repressor VAL1. In the wildtype FLC locus the localisation of VAL1 promotes transcriptional silencing through histone deacylation through interaction with the conserved apoptosis- and splicing-associated protein (ASAP) complex. This study adds an additional layer of molecular complexity to the process of regulating the FLC locus and provides insight into the important role for primary sequence-specific targeting during gene silencing.

Bryant F, Munoz-Azcarate O, Kelly AA, Beaudoin F, Kurup S, Eastmond PJ (2016) Acyl carrier protein DESATURASE 2 and 3 are responsible for making omega-7 fatty acids in the aleurone Plant Physiology http://dx.doi.org/10.1104/pp.16.00836 Open Access

Peter Eastmond (Rothamstead) leads this work that investigates the components that determine seed fatty acid content. Specifically Omega-7 monounsaturated fatty acids (ω-7s) are enriched in the aleurone of Arabidopsis seeds so this study used a Multiparent Advanced Generation Inter-Cross population to identify a QTL linked to ω-7 content that includes the ACYL-ACYL CARRIER PROTEIN DESATURASE1 (AAD1) and AAD3 genes. AAD family members possess both stearoyl- and palmitoyl-ACP Δ9 desaturase activity and aad3 mutants show a significant reduction in ω-7 content, which is common with mutants in other AAD family members. In addition the authors show that the FATTY ACID ELONGASE1 protein is required for accumulation of long-chain ω-7s in the aleurone. Overall this research provides new insight into the pathway that produces ω-7s in the aleurone, indicating that these genes might represent a target for future strategies to alter seed fatty acid content.

Wang P, Richardson C, Hawes C, Hussey PJ.(2016) Arabidopsis NAP1 Regulates the Formation of Autophagosomes Current Biology http://dx.doi.org/10.1016/j.cub.2016.06.008

NAP1_pic
From http://www.sciencedirect.com/science/article/pii/S0960982216306200

This is collaborative effort between the labs of Patrick Hussey (Durham) and Chris Hawes (Oxford Brookes) investigates the role of the NAP1 protein, which is a member of the SCAR/WAVE complex, on the formation of autophagosomes. These organelles are induced by certain stress conditions and fewer are produced in nap1 mutants after starvation stress. This also corresponds to wildtype NAP1 localisation. Concomitantly nap1 mutants, as well as mutants of other members of SCAR/WAVE complex, are more suspectible to nitrogen starvation and is less tolerant to salt stress. The best characterised role of the SCAR/WAVE complex is during ARP2/3-mediated actin nucleation yet this study demonstrates an addition function as a regulatory of autophagy.

Lim B, Smirnoff N, Cobbett CS, Golz JF (2016) Ascorbate-Deficient vtc2 Mutants in Arabidopsis Do Not Exhibit Decreased Growth Front Plant Sci. 7:1025

http://dx.doi.org/10.3389/fpls.2016.01025 Open Access

Nick Smirnoff (Exeter) is a co-author on the Australian-led research into Arabidopsis vtc mutants, which have a significant reduction in ascorbate-acid levels. Ascorbate is synthesized via the L-galactose pathway, the first enzyme of which is encoded by the paralogs VITAMIN C2 (VTC2) and VTC5. This study characterises the growth of a vtc2 T-DNA mutant that has a 30% reduction in ascorbate levels. Surprisingly this does not result in any signficant phenotypic and they suggest that a previously characterised growth reduction in other vtc2 mutant alleles is likely due to unknown genetic lesions.

ICAR2016 Meeting Report: William Broad

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Published on: August 5, 2016

Submitted by William Broad (University of Oxford)

I was very grateful to receive a travel bursary from the Gatsby Foundation and GARNet to attend the International Conference on Arabidopsis Research 2016 (ICAR2016), held in the city of Gyeongju, South Korea. The location and number of attendees gave this event a much different atmosphere and made for a unique experience in comparison to the small subject-specific gatherings I have attended in the UK. While even small conferences attract an international audience, due to their locations, they are typically populated by those living just a cheap flight away. Therefore when attending a conference on the other side of the planet, with the vast majority of delegates coming from Korea, China, and Japan, it was amazing to discover the cutting edge research that is occurring in East-Asia.

ICAR2016 offered a great opportunity to delve deeper into my own field of organellar biology, as well as to become acquainted with the areas of research that simply attracted my attention. Indeed, there were many interesting talks and here I will briefly highlight a few memorable speakers.

JenSheenThe conference opened with a key note lecture delivered by Professor Jen Sheen, who began in contrast to the typical fashion of justifying why plant science is important, by displaying some of her own craftsmanship of photography and horticulture, to instead remind us how diverse and beautiful plants really are. Professor Sheen has spent much of her career delving into the world of how sugars, mainly glucose and also nitrates, act as a signalling molecules in plants. Dissecting this process is truly an interesting topic for a cell biologist, these processes are important to organisms at a multitude of levels, and critically they are not static, and are among a tangle of interconnections. Professor Sheen’s description of these processes made for an excellent talk at the cutting edge of molecular biology.

In organellar biology I was excited to meet Dr. Jesse Woodson, who presented the findings of his recent Science paper (Woodson JD, et al. 2015. Science 350:450-4) together with some previously unseen data. Jesse and colleagues from Professor Joanne Chory’s lab, has found that stressed chloroplasts can be selectively degraded by the vacuole, something not previously observed, and that this process is triggered in part by a cytosolic ubiquitin-proteasome system E3 ligase called PUB4. A really cool piece of this talk was the 3-D image of the engulfment process generated by TEM, which offers far more detail and insight than the 2D representation. This work raises interesting questions regarding how the chloroplast can communicate its stressed state externally to the cytosol and how that results in it being specifically selected for degradation by the vacuole.

An unexpected highlight for me was the work presented by Professor Ikuko Hara-Nishimura, whose lab’s research focus is on the directional growth and movement of plants. She presented data regarding a group of regulatory factors of such movement – components of the cytoskeleton, mysosins XIf and XIk, and Actin8. Mutants of these proteins exhibit hyper-bending in response to gravity, the plants therefore seem to overshoot their reorientation as if there is nothing to put the brakes on once bending has been triggered. Curiously, in at least one of these mutants the circadian up and down oscillation of Arabidopsis rosette leaves is absent, a finding punctuated by an enthusiastic attendee sitting behind me booming ‘That is interesting! That’s Really interesting!’.

On the last day of the conference I was able to see a talk by Professor Harvey Millar, which was on plant proteomics. Specifically with regard to how the proteome of the Arabidopsis leaf changes over time during growth, what the turnover rates of individual plant proteins are, and even calculation of the energy cost of protein turnover in different leaves. What could have come across as a mundane stamp-collecting aspect of biology was presented as something much more, the results of which appear to give great insights into how these plants manage this aspect of their economy during growth.

Broad_13599898_10153845726471676_7147785929705411430_nFinally, it is important not to forget the value of meeting fellow researchers, the coffee breaks and evenings spent at the bar were as appreciable as attending the talks. As a young researcher I found attending ICAR2016 to be a formative experience. I was able to see first-hand what my fellow researchers are doing and how they are doing it, put faces to the names atop the papers I’ve been reading, and discuss science with fellow PhD students, post-docs, PIs and long established professors. I was able to gain exposure to new ideas in research and, as I was privileged enough to give a presentation, I received helpful feedback on my own work. My experiences there really turned the competitive publish-or-perish mentality of science on its head and revealed a community of interested people driven by curiosity.

Arabidopsis Research Roundup: July 27th

Each of the papers in this Arabidopsis Research Roundup involves the response to different stimuli. Giles Johnson at Manchester provides an audio description of work that has discovered a novel mechanism of cold sensing whilst Gordon Simpson and John Brown from Dundee are contributors to work that has interrogated the sugar signaling pathway. Finally is a study from Warwick that has identified novel loci involved in ABA signaling and seed vigour.

Dyson BC, Miller MA, Feil R, Rattray N, Bowsher C, Goodacre R, Lunn JE, Johnson GN (2016) FUM2, a cytosolic fumarase, is essential for acclimation to low temperature in Arabidopsis thaliana Plant Physiology http://dx.doi.org/10.1104/pp.16.00852

Open Access

From http://www.plantphysiol.org/content/early/2016/07/20/pp.16.00852.long
From http://www.plantphysiol.org/content/early/2016/07/20/pp.16.00852.long

Giles Johnson (Manchester) is the corresponding author on this UK-German collaboration that looks at the mechanisms by which plants sense the low temperatures that cause significant phenotypic changes. GC-MS showed that fumarate is a key component in the cold tolerance response and that the activity of the FUM2 enzyme is responsible for accumulation of fumaric acid. Plants that lack FUM2 activity show significant alteration in gene expression and metabolite profile following a cold treatment and in particularly are unable to acclimate photosynthesis at lower temperatures. Therefore this study introduces a novel component of the temperature sensing apparatus, which might have broad significance for attempts to develop crops with an improved cold response.

Giles kindly provides an audio description of this work, which includes an overview into cold acclimation of photosynthesis. This includes an excellent ‘stress-ball’ analogy! (Apologies for pen-clicks :/).

 

Carvalho RF, Szakonyi D, Simpson CG, Barbosa IC, Brown JW, Baena-González E, Duque P (2016) The Arabidopsis SR45 Splicing Factor, a Negative Regulator of Sugar Signaling, Modulates SNF1-Related Protein Kinase 1 (SnRK1) Stability The Plant Cell http://dx.doi.org/10.1105/tpc.16.00301

From http://www.plantcell.org/content/early/2016/07/19/tpc.16.00301.abstract
From http://www.plantcell.org/content/early/2016/07/19/tpc.16.00301.abstract

Gordon Simpson and John Brown (James Hutton Institute) are contributors to this Portuguese-led study that investigates the role of the SR45 splicing factor in sugar signaling. In sr45-1 mutants they show that glucose-feeding causes increased levels of the energy-sensing SNF1-Related Protein Kinase 1 (SnRK1) yet without increasing its gene expression. Concomitantly the hypersensitivity of sr45-1 mutants is rescued in plants with reduced levels of SnRK1. The authors discovered that the mechanistic link between these genes involves SR45-1 regulating the alternative splicing of the 5PTase13 gene, which encodes an inositol polyphosphate 5-phosphatase that interacts with SnRK1 in vivo. In wildtype plants 5PTase13 modulates proteasomal-mediated degradation of SnRK1 and therefore a perturbation of this process in sr45-1 explains this defect in sugar-sensing.

Morris K, Barker GC, Walley PG, Lynn JR, Finch-Savage WE (2016) Trait to gene analysis reveals that allelic variation in three genes determines seed vigour. New Phytol. http://dx.doi.org/10.1111/nph.14102 Open Access

Bill Finch-Savage is the corresponding author on this study from the Warwick University that uses Brassica oleracea natural variation to identify novel loci involved in seed vigour. The discovered QTL was termed Speed of Germination (SOG1) and contained two genes, BoLCVIG2, a homologue of the alternative-splicing regulator (AtPTB1) and BoLCVIG1, which has unknown function. Transfer of these alleles into Arabdopsis causes alterations in seed germination, which is also observed in mutants of the equivalent Arabidopsis genes (At3g01060, At3g01150). Furthermore an additional discovered QTL encodes the Reduced ABscisic Acid 1 (RABA1) gene, which influences ABA content and seed vigour. Therefore this mapping strategy has discovered three genes that promote seed vigour resulting from alterations in ABA content and sensitivity.

ICAR2016 Student Perspective: Marie Bruser

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Published on: July 26, 2016

Thanks to Marie Bruser for putting together her thoughts from the ICAR2016 meeting.

The annual Arabidopsis conference was held in GyeongJu in South Korea this year. I was fortunate to go, thanks for some extra funding from the Gatsby Foundation and GARNet.

HICO_Bruser
Going to the conference I of course looked forward to my own supervisor Lars Østergaard’s talk. But I also had some other sessions and speakers I was really excited about. And they did not disappoint. Sabrina Sabatini wonderfully explained her elegant model of auxin and cytokinin distribution in the root, Dolf Weijers showed some stunning images of the Arabidopsis embryo which were only rivalled by Minako Ueda with her live-cell imaging of cell divisions, microtubule arrangement and mitochondria in the zygote. There was also Annika Weimer from the Bergmann lab who told the story of how formative divisions occur in the root and the stomata, followed by a great description of the sepal cellular arrangements by Adrienne Roeder. She outlined the effect of ATML1 levels on cells division versus endoreduplication.

Tom Beeckman’s talk was also great where he presented his Science paper, published in January, on a cyclical auxin signal coupled to cell death which determines lateral root formation. I had read his paper and discussed it in a journal club but it was brilliant to hear the story told by the person most excited and motivated about it! One of the most important things I learned from these sessions was not to dismiss Domains of Unknown Function (DUFs). Hunting down a DUF, Dolf Weijers and his lab found a protein beautifully localized in the corner of cells, playing a role in determining the cell division plane. And who wouldn’t want to name a protein!?

I also want to highlight two talks from the transporter session, a topic not directly relevant to what I do. Yi-Fang Tsay neatly described her research on nitrogen transporters. She identified one that was involved in transporting N from old to new plant parts in times of low N (NRT1.7) and others that transported nitrogen in high N conditions (NRT1.11 and NRT1.12). The other talk, by José A Féijo, showed that transport in the plant can be a lot more complex, with a large network of genes involved in calcium transport in the pollen tube.

But for me the best talk came from a very relaxed and confident John Bowman in the session on shoot development. His theory that leaves are modified shoots has led him to attempt to modify leaves in a way that they revert back to the indeterminate growth of shoots. And he has succeeded, producing Arabidopsis leaves that are crinkled, a little like kale, and grow indeterminately. His talk was delivered in a very clear manner and kept me fascinated all the way through, even though he was the last of his session. And even though it was my favourite talk, it was one I took the fewest notes on and I believe that is because I was so captivated by his story that I just sat back and listened and simply forgot about notetaking!
PIN_BruserAnd there is one more thing I really got to appreciate at this, my first large conference: that the talks are just one part of the event. The few hours you get around the talks; during coffee and lunch times, dinner, poster sessions and drinks, are the times that probably matter just as much. They give you the chance to talk to the people you have just seen present. They give you the chance to meet people you admire and talk to them on a first name basis. They allow you to meet scientists from all over the world, from all career stages. They make you realise that everyone else, same as you, is there to have a great time talking science and experiencing a different country. And most of all, it makes you appreciate that in the end, no matter what stage of your career you are, you are part of a community that is interested in a common topic, driven by curiosity and a thirst for knowledge.
Mix_Bruser

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
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