Arabidopsis Research Roundup: January 29th

This weeks Arabidopsis Research Roundup features a paper from David Baulcombe and Joe Ecker that further deciphers mechanisms of RNA silencing and is kindly discussed by postdoc Mat Lewsey in a short audio description. Elsewhere there are three studies that include researchers from CPIB in Nottingham. Leah Band contributes to a study that links environment sensing, cell death and auxin signaling whilst Ive De Smet leads a study that finds new proteins involved in cell division. Malcolm Bennett and John King take a modeling approach to describe auxin signaling via the GH3 protein family. Finally Frank Menke leads a study that provides more detail into Pattern Recognition Receptor (PRR) mediated immune signaling and then Jim Dunwell participates in a paper that describes a new method of analyzing GWAS data.

Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR (2016) Mobile small RNAs regulate genome-wide DNA methylation. Proc Natl Acad Sci U S A. Open Access

Over the past few years RNA-mediated silencing has emerged a key mechanism for the control of gene expression. This study is a collaboration between the lab of Sir David Balcombe (Cambridge) and Joe Ecker at the SALK institute in California. Mat Lewsey, who is a British postdoc working with Professor Ecker, kindly provided a short audio description of the paper.

These groups have previously shown that sRNAs are highly mobile throughout the plant. This study shows that thousands of loci expressed in roots are dependent on mobile sRNAs generated from the shoot. They unpick the genetic basis of this response showing that it is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) but not CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. They also show that mobile sRNAs are resposible for the silencing of TEs that are found in gene-rich regions, although this is not a physiologically important response in Arabidopsis, which contains a relatively small amount of transposon tissue. Interestingly they a show that sRNAs generated from different Arabidopsis ecotypes are able to move across graft junctions and can cause methylation in usually unmethylated regions.

PNASpicXuan W, Band LR, Kumpf RP, Van Damme D, Parizot B, De Rop G, Opdenacker D, Möller BK, Skorzinski N, Njo MF, De Rybel B, Audenaert D, Nowack MK, Vanneste S, Beeckman T (2016) Cyclic programmed cell death stimulates hormone signaling and root development in Arabidopsis. Science . 351(6271):384-7

This study is led by Tom Beeckman from Gent University and features Leah Band from CPIB in Nottingham. They reveal an exciting relationship between cell death in root cap cells and hormone signaling. The root cap is a protective tissue that overlies the Arabidopsis root tip and might be considered as an ‘inactive’ tissue. However this study shows that an auxin signal released from root cap cells sets the spacing of lateral organs along the root. As root cap cells move up the root they undergo programmed cell death, which in turn releases a pulse of auxin and establishes a pattern of lateral root formation. The authors suggest that this relationship might integrate external soil conditions so that lateral roots will develop to optimise uptake of water and nutrients. It is well known that an auxin signal simulates lateral root formation but this study provides an explanation as to the genesis of this signal and its integration with external environmental factors.

Yue K, Sandal P, Williams EL, Murphy E, Stes E, Nikonorova N, Ramakrishna P, Czyzewicz N, Montero-Morales L, Kumpf R, Lin Z, van de Cotte B, Iqbal M, Van Bel M, Van De Slijke E, Meyer MR, Gadeyne A, Zipfel C, De Jaeger G, Van Montagu M, Van Damme D, Gevaert K, Rao AG, Beeckman T, De Smet I (2016) PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root. Proc Natl Acad Sci U S A.

This broad collaboration between US-UK and Belgian researchers is led by Tom Beeckman and Ive De Smet, who works at CPIB in Nottingham. In addition it includes a contribution from Cyril Zipfel at TSL. This study aimed to identify proteins that interact with the plasma membrane-localized receptor kinase ARABIDOPSIS CRINKLY 4 (ACR4), which plays a role in the control of cell division in the Arabidopsis root. They find that PROTEIN PHOSPHATASE 2A-3 (PP2A-3), a catalytic subunit of PP2A holoenzymes interacts with ACR4 and has a previous uncharacterised role in control of formative cell divisions. The authors show that the biochemical network that links ACR4 and PP2A-3 is regulated by phosphorylation.

Mellor N, Bennett MJ, King JR (2016) GH3-Mediated Auxin Conjugation Can Result in Either Transient or Oscillatory Transcriptional Auxin Responses. Bull Math Biol.

This paper led by Professor Malcolm Bennett and John King from CPIB is an example of the growing number of multi-disciplinary interactions between biologists and mathematicians. Here a model is developed that interrogates auxin signaling and homeostasis through the GH3 gene family. This includes a parameter that considers auxin transport via the LAX3 influx protein, which, together with the activity of GH3 proteins can facilitate a positive feedback loop that allows cells to response to excess auxin.

Mithoe SC, Ludwig C, Pel MJ, Cucinotta M, Casartelli A, Mbengue M, Sklenar J, Derbyshire P, Robatzek S, Pieterse CM, Aebersold R, Menke FL (2016) Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase. EMBO Rep. Open Access

Frank Menke (TSL, Norwich) is the leader on this collaboration between UK, Dutch and Swiss researchers that investigates innate immunity signaling mediated via Pattern Recognition Receptors (PRRs). Tight control of this signalling is very important to prevent spurious activation of the immune response. These authors find that the differentially phosphorylated MKKK7 can interact with the FLS2 protein, which is key in the perception of bacterial flagellin. In turn MKKK7 attenuates the signalling of a downstream MAPK that contributes to defence-related gene expression. Therefore the show that the FLS2-MKKK7 signaling module is critical for control of innate immunity.

Wang SB, Feng JY, Ren WL, Huang B, Zhou L, Wen YJ, Zhang J, Dunwell JM, Xu S, Zhang YM (2016) Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology. Sci Rep. Open Access

Professor Jim Dunwell (Reading) is a UK contributor to this largely Chinese publication that introduces a new method to analysis GWAS-style data. They propose an analysis based on random-SNP-effect MLM (RMLM) and a multi-locus RMLM (MRMLM) and using stimulations show that their new method can be powerful than conventional types of analysis. To test the method they analysed flowering time traits in Arabidopsis and detected more genes that were involved in the process.

For those interested in different-types of GWAS analysis, Professor David Salt introduced another new method during a recent ARR.

New Phytologist Symposia: 2016

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Published on: January 26, 2016

The New Phytologist Trust have been organising Plant Science Symposia for the last 20 years and in 2016 will see the 37th and 38th events, which take place in Beijing and Bristol respectively. These relatively small, focussed meetings bring together experts on the particular topic for exciting information and discussions. For more information please see below and check out the links:

37th New Phytologist Symposium: Plant Developmental Evolution

15th-19th May 2016

Beijing, China

Travel grant submission deadline: Thursday 25th February 2016

Poster abstract submission deadline: Thursday 17th March 2016

37th-NPS-(Web-Medium)-1000-x-1000-(2714)The relatively new field of plant evolutionary-developmental biology (‘evo-devo’) seeks to understand how and why plant morphological characters have evolved to produce the tremendous diversity of form in living plants. This meeting will draw together researchers in plant evo-devo for exchange of ideas, current research, and discussion of future directions for the field.

Sessions: floral development; vegetative meristems, leaves, and inflorescences; plasticity and life history evo-devo; selected poster abstract talks.

Eighteen leading scientists will speak at the Symposium. We hope that this will stimulate focused discussion and the exchange of ideas at what will be a relatively small (around 120 delegates) and informal meeting. There will be a poster session, selected talks, discussion and a conference dinner.

Keynote speakers: Beverley Glover, University of Cambridge, UK; Mark Rausher Duke University, USA; Miltos Tsiantis, Max Planck Institute for Plant Breeding Research, Germany.


38th New Phytologist Symposium: Colonization of the terrestrial environment

25th-27th July 2016

Bristol, UK

Travel grant submission deadline: Thursday 21st April 2016

Poster abstract submission deadline: Thursday 19th May 2016

38th New Phytologist Symposium - logo_MediumThe purpose of this symposium is to explore the contribution that plants and mycorrhizal fungi made to the colonization of the terrestrial environment. Building on the success of the 25th New Phytologist Symposium, the focus will be on exploring current uncertainties in four major themes:

1) Interrelationships;

2) Anatomy – developmental genetics;

3) Refining biogeochemical models to take account of the role of plants and fungi;

4) Anatomy and physiology of early land plants – what can we learn from extant species?

The meeting will take place over three days in Bristol, UK. There will be a number of invited and selected talks (chosen from submitted poster abstracts) and also be dedicated time for a poster session and conference dinner.

Keynote speakers: Liam Dolan, University of Oxford, UK; Ned Friedman, Harvard University, USA; Tim Lenton, University of Exeter, UK


Call for Symposia

New Phytologist very impressively schedule future Symposia almost two years in advance and they already have titles and dates set for the 39th and 40th meetings.

Therefore if you have a great idea for your own symposium please contact The New Phytologist Trust as they are accepting proposals. They have funding up to £43,000 from 2018 onwards. The deadline for proposals is 28th February 2016. Read more here:



Arabidopsis Research Roundup: January 22nd 2016

A mixed selection of research in this UK Arabidopsis Roundup. Firstly a study from Stefan Kepinski and Mark Estelle that adds another layer of understanding to the regulation of the auxin response. Enrique Lopez-Juez leads a study into signaling between the nucleus and chloroplast while Tracey Lawson contributes to an investigation into role of starch metabolism in guard cells. Fran Maathuis and co-worker looks at differences in vacuolar transport between Arabidopsis ecotypes while Alan Marchant is involved in a study of cell wall pectins. Finally William Amos has uses the 1001genomes project to investigate heterozygote instability (HI).

Wang R, Zhang Y, Kieffer M, Yu H, Kepinski S, Estelle M (2016) HSP90 regulates temperature-dependent seedling growth in Arabidopsis by stabilizing the auxin co-receptor F-box protein TIR1. Nat Commun. 5;7:10269. Open Access

Stefan Kepinski (Leeds) is the UK lead on this collaboration with Mark Estelle from UCSD and it continues their previous work that investigates the much-studied auxin receptor TIR1. Arabidopsis seedlings grown at 29C show auxin-dependent hypocotyl elongation although the molecular mechanism behind this response has remained opaque. In this study they show that in high temperatures TIR1 accumulates in a manner dependent on the molecular chaperone, HSP90. In addition HSP90 and the co-chaperone SGT1 directly interact with TIR1. Inhibition of HSP90 results in degradation of the TIR1 and causes a range of auxin-mediated growth processes at both high and low temperatures. This study adds another level of complexity to the molecular basis of the auxin response.

Hills AC, Khan S, López-Juez E (2015) Chloroplast Biogenesis-Associated Nuclear Genes: Control by Plastid Signals Evolved Prior to Their Regulation as Part of Photomorphogenesis. Front Plant Sci. 10;6:1078. Open Access

The work comes exclusively from the lab of Enrique Lopez-Juez at Royal Holloway and investigates at the expression of photosynthesis-associated nuclear genes (PhANGs). This expression is dependent on light as well as plastid-to-nucleus “biogenic” communication signals and causes the assembly of photosynthesis component chloroplasts. The authors investigate the factors that control the activity of the Lhcb promotor in the light and the dark, both in angiosperms and gymnosperms. They propose that suppression of PhANG responses has contributed to the evolution of light-controlled chloroplast biogenesis.

Horrer D, Flütsch S, Pazmino D, Matthews JS, Thalmann M, Nigro A, Leonhardt N, Lawson T, Santelia D (2015) Blue Light Induces a Distinct Starch Degradation Pathway in Guard Cells for Stomatal Opening. Current Biology
Graphical Abstract
Tracey Lawson (University of Essex) is the UK lead on this UK-French-Swiss study that uses the stomatal guard cell experimental system to investigate the role of carbon metabolism in the response to blue light. Interestingly guard cells differ from other leave tissues in that they contain starch at the end of the night. However this starch store is rapidly degraded within 30minutes of light and is important for stomatal opening and subsequent biomass production. This starch degradation involves action of two enzymes, β-amylase 1 (BAM1) and α-amylase 3 (AMY3) that do not function during night time starch degradation in other tissues. This process is coordinated by blue light signalling and correlates with the activity of a plasma membrane ATPase. This study adds yet another level of our understanding into the mechanism of stomatal opening. See image for a proposed model of this process (from Cell Press).

Hartley TN, Maathuis FJ (2015) Allelic variation in the vacuolar TPK1 channel affects its calcium dependence and may impact on stomatal conductance. FEBS Lett. 90(1):110-7

Fran Maathuis (University of York) is the leader on this study that assesses the transport properties of two different vacuolar-localised AtTPK1 alleles identified for a study of natural variation in Arabidopsis. They use patch-clamping the interrogate the difference between these proteins from Lansberg (Ler) and Kas-2 ecotypes, when they showed different levels of Ca(2+) dependence. This coincided with lower water loss in either the presence of absence of ABA and higher Ler AtTPK1 activity at similar cytoplasmic [Ca]. The authors present a model that helps to explain their findings.

Dumont M, Lehner A, Vauzeilles B,, Malassis J, Marchant A, Smyth K, Linclau B, Baron A, Mas Pons J, Anderson CT, Schapman D, Galas L, Mollet JC, Lerouge P (2015) Plant cell wall imaging by metabolic click-mediated labelling of rhamnogalacturonan II using azido 3-deoxy-D-manno-oct-2-ulosonic acid. Plant Journal.

The majority of the authors on this Technical Advance are from French institutions but also includes UK plant scientist Alan Marchant (University of Southampton). They investigate the chemistry of Arabidopsis and tobacco cell walls, specifically looking at the incorperation of 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo), a monosaccharide that is only found the cell wall pectin rhamnogalacturonan-II (RG-II). They show that RG-II is found in the primary cell wall including within the root elongation zone. Finally they show that monitoring of Kdo is an effective way to study the synthesis and redistribution of RG-II during root growth.

Amos W (2015) Heterozygosity increases microsatellite mutation rate. Biol Lett. Open Access

This study is led by Professor William Amos who is based in the Zoology department at Cambridge. He is not usually a plant science researcher but used the excellent 1001genome project to investigate heterozygote instability (HI) in Arabidopsis. He looked at AC microsatellite sequences from over 1100 genome sequences and used rare alleles as a surrogate for more recent mutations, ultimately showing that rare alleles are more likely to occur at locus-population combinations with higher heterozygosity even when all populations carry exactly the same number of alleles. This shows that local heterozygosity causes more mutations and represents a positive feedback loop.

GARNet/Egenis Workshop: Integrating Large Data into Plant Science: From Big Data to Discovery

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Published on: January 13, 2016

GARNet and the Exeter Centre for the Study of the Life Sciences (Egenis) are hosting a two-day workshop on ‘Integrating Large Data into Plant Science: From Big Data to Discovery’ to be held in the picturesque Dartington Hall, Totnes, Devon on April 21st-22nd 2016.

The aims of this workshop are to:
1. Introduce examples of how researchers have re-used datasets in innovative ways.
2. Examine the intrastructure that exists to support the re-use of large datasets
3. Discuss the mechanisms by which the community deals with big data.

As you can see below we have an exciting program with speakers from across academia, industry and the scientific journals. Download the PDF version here: GARNet/EgenisPoster

We have kind support from the ERC and the BBSRC so registration for this workshop will be free although we will be limiting the number of delegates to around 50. Therefore if you are interested in attending please contact the GARNet coordinator Geraint Parry ( with a short paragraph outlining why this workshop would be useful to you. Submitting your application early will allow you to benefit from a reduced rate for accommodation at Dartington Hall.




Report from UKPSF Working Groups

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Published on: January 12, 2016

In 2014 the UK Plant Science Federation (UKPSF) published a report on ‘Current Status and Future Challenges‘. This report included a recommendation to establish four ‘Working Groups’ that would investigate future directions for UK plant science under these broad areas:

– Training and Skills

– Funding

– Translation

– Regulation

At the end of 2015 the results of these working groups were published in PDF format on the UKPSF blog along with a brief analysis of their content by Dr Sandy Knapp from the Natural History Museum. As Sandy did a great job there is no need to repeat this analysis but GARNet has put together a brief single page PDF summary:


One real outcome from these working groups is the establishment of a consultatation period that will then produce a Roadmap for UK Plant Science for the next 25 years. This comprehensive document aims to be published by mid-2016 and the invitations to attend discussion groups in London and York will go out in the next few weeks. Hopefully this Roadmap will have as successful an impact as a similar project did which focussed on the UK capacity for Synthetic Biology. Fingers crossed!



UK Arabidopsis Research in 2015.

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Published on: January 12, 2016

Over the past few years, GARNet has kept track of papers (in the <a href="http://blog.garnetcommunity comparaison prix” target=”_blank”>ARR) that are published by UK researchers and feature Arabidopsis work of one sort or other.  When we look back over 2015 we documented 152 different papers featuring UK researchers, even though we probably miss one or two papers along the way.

When we look at the distribution of these papers it is unsurprising that Plant Physiology has the most papers given the size of each months edition. Other usually popular journals also feature toward the top: The Plant Cell, New Phytologist, Plant Journal and PLoS One. It is perhaps surprising that Journal of Experimental Botany (JXB) hasn’t had more Arabidopsis papers from UK researchers but this is likely due to the broader remit of that journal.

Overall approximately 70% of these papers are Open Access which seems to be good news for the communication of research from our Universities. Relatedly, in 2014 GARNet published a broader analysis of Publication Trends for Arabidopsis work that can be found here.

ARR_2015Note that only journals with two or more publications are included on this graph.

Mathematics in the Plant Sciences Study Group

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Published on: January 11, 2016

The very mention of differential equations or any other associated type of mathematics can be enough to have many biologists break into a cold sweat! I think it’s fair to comment that the prevailing opinion in the past has been that maths is ‘too complicated’ and that it doesn’t have ‘any relevance’ for their work.

However this idea is slowly changing with the appearance of more mathematic modeling in biological manuscripts and the need for cross-disciplinarity in grant applications. In basic terms, a partial differential equation aims to measure how parameters changes with respect to one another: which is exactly what any biologist is always studying. Therefore your research should, to a greater or lesser extent, be relevant for mathematical interrogation.

Therefore in order to facilitate interactions between biologists and mathematics, the ‘Mathematics in the Plant Sciences Study Group (MPSSG)’ was inaugurated in 2007 as part of the initial funding for the Centre for Integrative Biology (CPIB) at Nottingham University. Over the past 9 years these study groups have been extremely successful and have even directly led to a publication, which modeled the biomechanical parameters that are involved in anther opening (Nelson et al, New Phytologists, 2012, doi: 10.1111/j.1469-8137.2012.04329).

The 7th MPSSG was held in Nottingham between Jan 4th-7th and took the same successful format as in other years. At the start of a meeting, three biologists presented a problem connected to their research, which had been selected by the organisers as being amenable for inclusion in this process.

As described below, these problems varied across the breadth of plant sciences so as to attempt to discriminate between the type of mathematics that might be applied to each case. After the initial presentations the biologists moved to seminar rooms where they were joined by a small group of mathematicians who are interested in modeling their problem. Over the course of the study group this evolved nicely as the mathematicians settled on a project that they were most interested in investigating. Most of these researchers were based in Nottingham although there were visitors from other UK and International universities.

On day one the discussions resembled a formal seminar session where the biologist led the mathematicians through the background of their problem. This is an interesting process as the mathematicians obviously had a very limited knowledge of each specific system, even though they might have some experience in modeling biological problems.
I observed this process for two of the study groups and it struck me that there was a tipping point at which time the mathematicians had taken onboard enough information about the problem to start to develop their own ideas. Suddenly at this point there were partial differential equations written on the whiteboard as the process began in earnest……

From this time onward the biologist plays a more advisory role whereas the mathematicians put in the hard work of transferring their initial equations into their analysis-program of choice. This is not a rapid process as the next two days are spent discussing and refining these models before the findings are presented on the final afternoon, just four days after most of the attendees will have first learnt about the topic!

The overall aim of the study groups is to begin to develop a model that can mathematically represent what is observed within the biological information.

In the initial stages of the process, I was somewhat surprised by how freely the mathematical ideas were discussed. In my experience, many biology-based discussions are often constrained by the need for an absolute requirement for the presence/absence/expression of a particular protein or gene in order to develop a hypothesis. However the mathematicians were unencumbered by this requirement and rather were able to throw ideas around, seeing what, if anything, would eventually stick. This ultimately might lead them blindly down closed alleyways but not always. Importantly it was clear that these discussions made the biologists look at their problem in a different way and each of the participating speakers had a list of future experiments that had resulted from these discussions.

More detail about the three problems presented in this study group can be found on the MPSSG website but in summary:

Biosynthesis of Casparian strips: How to build a micron-scale bridge out of a lignin polymer? Presented by Dr Guilhem Lenaic (University of Aberdeen).

The molecular participants that play a role in the generation of the casparian strip (CS) are not well studied. Guilhem works in the lab of GARNet chair Professor David Salt and introduced the genes that are involved in this process and importantly, the patterns of CS that develop in different mutant plants. Simply put, the CS is a band of lignin that surrounds root endodermal cells ‘like an belt’ and plays an impCSPicortant role in water uptake, which is of clear importance not only for the growth of an individual plant but has broader relevance for issues of water use efficiency. The CS develops through a series of patterning steps that have at been, in part, genetically determined. Therefore the mathematicians attempted to develop a model that generated these patterns by parametrising the activity of different proteins as well as a monolignol lignin precursor molecule.

Ultimately they made some process developing both 1D and 2D models although, as with all the problems from the study group, there was still work to do. Arguably the best line from the presentation, used to account for a stray equation and was described as “classic-MPSSG”, was “oh yes…..that line was written on the whiteboard by John King…..but then he left….”.

Modeling Leaf-Sheath Interactions in Grasses. Presented by Dr Douglas Cook (NYU Abu Dhabi).

This problem introduced the biomechanical interaction between a maize sheath and the leaf that wraps itself around the sheath, providing protection and mechanical strength to the underlying tissue. The leaf surrounds the sheath prior to internode elongation, so when the sheath start to elongate there is a frictional interaction between SheathPicsheath and leaf. This can result in ‘slippage’ when the forces between sheath and leaf build up. Dr Cook mentioned that can is an economical important parameter as without the protective influence of the leaf, the maize stalk is weak and can be more easily bent.

Initially the mathematicians presented this problem as being equivalent to the interaction between two cylindrical tubes. Over the course of the workshop a number of models were developed, not all of which were successful but which highlighted the important trial-and-error nature of many of these interactions. A nice analogy for this process was the comparison to the seismic activity that builds up between tectonic plates. A favourite comment from the early discussions occurred when the sheath was described as an “infinite cylinder”…. certainly not the type of language commonly heard when discussing plant science problems!

Hyperspectral image analysis of plants, presented by Dr Andrew French (University of Nottingham)

Imaging with a hyperspectral camera (that records a complete breakdown of the reflectance spectra for each pixel in an image) provides a researcher with a large amount of data (5seconds=1Gb) but much of this is extraneous for use in any one particular biological problem. In this problem Dr French presented the idea that this type of data could be used to detect minute changes in the colour of leaves that are a prelude to visible signs of disease. Therefore the task for the mathematicians was to devise a way of analysing the spectral data to define a new indice that represents a relationship between wavelengths that has the most utility for this type of analysis. I did not directly observe any of the interactions of this group but they appeared to make good progress. In their final presentation the description of their methods was the most mathematically dense of the three problems (at least to a naïve observer such as myself). However the group had clearly put together some ideas that could be developed in future.

FrenchPicThe final step in the process is to collate the information from each study group into a report, which will be published on the CPIB website. Later on this will hopefully yield further interactions and potential grant writing opportunities between the biologists and mathematicians involved in the meeting.

Please look out for a summary of the final reports in the next edition of the GARNish newsletter, to be published in the summer. From a biologists perspective I would encourage anyone who is wary of interacting with mathematicians, computer scientists or modellers to bite the bullet and make that connection. Even though your system ultimately might not be the most amenable to a modeling approach, the interaction will help you develop ideas that will undoubtedly drive your research forward in unexpectedly directions. Basically it is a no-lose interaction!

Arabidopsis Research Roundup: January 8th

For the inaugural Arabidopsis Research Roundup of 2016 we feature the final publications of UK researchers from 2015. Martin Howard kindly provides an audio description of a paper that looks at a fundamental aspect of transcriptional regulation, through the lense of the FLC gene, whilst his co-author Caroline Dean on that paper is an author on another manuscript that investigates RNA stability in the same FLC locus. Katja Graumann leads a paper that looks into gene expression at the periphery of the nucleus whilst Ian Colbeck looks at the effect of silver nanoparticles on plant growth. Ari Sadanandom is the UK lead of a study that investigates of SUMOylation and Ian Fricker looks at the role of a cytochrome P450 on the defence response. Finally Liam Dolan is involved in a comparative analysis of the genes involved in tip growth in the cells of plants and moss.

Wu Z, Ietswaart R, Liu F, Yang H, Howard M, Dean C (2015) Quantitative regulation of FLC via coordinated transcriptional initiation and elongation. Proc Natl Acad Sci U S A. Open Access

Martin Howard and Caroline Dean lead this study that comes out of the John Innes Centre and is the result of the same collaboration that featured in an ARR earlier in 2015. In this study they investigate the mechanisms that control the quantitative regulation of gene expression by focusing on the complex regulation of the FLOWERING LOCUS C (FLC). FLC expression is controlled by a chromatin silencing mechanism involving alternative polyadenylation of antisense transcripts. However they surprisingly show that the amount of RNA Polymerase II occupancy at FLC does not coincide very well with levels of FLC transcription. They used modeling to predict that there is a tight coordination between transcriptional initiation and elongation, which was validated by detailed measurements of the levels of FLC intronic RNA. Variation within initiation and elongation rates were significantly different and was coincident with changes in H3K36me3 and H3K4me2 levels in the FLC gene. The authors propose that chromatin state can influence transcriptional initiation and elongation rates and may be a general mechanism for quantitative gene regulation in a chromatin context.

Martin Howard kindly provides an audio description of this paper and wider aspects of transcriptional regulation.

Wu Z, Zhu D, Lin X, Miao J, Gu L, Deng X, Yang Q, Sun K, Zhu D, Cao X, Tsuge T, Dean C, Aoyama T, Gu H, Qu LJ (2015) RNA-binding proteins At RZ-1B and At RZ-1C play a critical role in regulation of pre-mRNA splicing and gene expression during Arabidopsis development Plant Cell

This study investigates a set of previously mysterious RNA-binding proteins and is led by Chinese researchers with a UK contribution from Caroline Dean (JIC). They look at two Arabidopsis proteins, AtRZ-1B and At RZ-1C that have RNA-binding domains and are localised to the mysterious nuclear speckles. In addition these proteins physically interact with a range of serine/arginine-rich (SR) proteins and disrupting this binding causes a range of growth phenotypes that are similar to that observed in At rz-1b/At rz-1c double mutants. These include delayed seed germination, reduced stature, and serrated leaves and on the cellular level this is accompanied by defective splicing and global changes in gene expression. Interestingly AtRz-1C directly effects the expression of the floral repressor FLC, which links this work with other research in the Dean lab. Overall this highlights the important role of At RZ-1B/1C in RNA splicing and the link to many developmental phenotypes.

Smith S, Galinha C, Desset S, Tolmie F, Evans D, Tatout C, Graumann K (2015) Marker gene tethering by nucleoporins affects gene expression in plants. Nucleus.

Expression of Seh1-LacI-YFP at the nuclear periphery. From
Expression of Seh1-LacI-YFP at the nuclear periphery. From

Katja Graumann and David Evans (Oxford Brookes) are the lead academics on this collaboration with the lab of Christophe Tatout from Clermont Ferrand in France. They are attempting to answer a long standing question in the field of the biology of the nucleus; whether genes that are located close to nuclear pore complexes have increased gene expression. They used the Lac Operator/ Lac Repressor (LacI-LacO) system to assess changes in gene expression when a loci is tethered to the NPC by attaching the LacI domain to the nucleoporins Seh1 or NUP50a. The Seh1 clones localised to the nuclear periphery and showed higher RNA and protein expression of Luc. When this interaction at the periphery was distributed, the higher levels of expression were abolished. The authors therefore show that association with the nuclear periphery is important for the regulation of gene expression.

Sosan A, Svistunenko D, Straltsova D, Tsiurkina K, Smolich I, Lawson T, Subramaniam S, Golovko V, Anderson D, Sokolik A, Colbeck I, Demidchik V (2015) Engineered silver nanoparticles are sensed at the plasma membrane and dramatically modify physiology of Arabidopsis thaliana plants. Plant Journal

Ian Colbeck (Essex) is the UK lead on this study that involves a collaboration between researchers in New Zealand, Belarus and Russia and focuses on the effect of silver nanoparticles (Ag NPs) on the growth of Arabidopsis seedlings. This type of nanoparticle is used for many difference applications so worries exist about the safety of their use. This study looks at the effect of Ag NPs on Arabidopsis root elongation and leaf expansion, both of which were inhibited at over [300mg/l] Ag NPs. In addition there were reductions of photosynthetic efficiency and accumulation of silver in plant tissues. They also showed that these particles altered the influx and efflux of metal ions whilst, although they were unable to catalyse hydroxyl radical generation, they did directly oxidise the major plant antioxidant, L-ascorbic acid. Overall the authors show that silver nanoparticles induce classical stress signalling responses but also illicit specific detrimental effects at the plasma membrane. At the whole plant level this study provides a worrying example for the role of Ag NPs on whole plant growth, even though the concentrations used in food preparation might be lower.

Crozet P, Margalha L, Butowt R, Fernandes N, Elias A, Orosa B, Tomanov K, Teige M, Bachmair A, Sadanandom A, Baena-González E (2015) SUMOylation represses SnRK1 signaling in Arabidopsis. Plant Journal

This pan-European study features researchers from Portugal, Austria and the UK’s Durham University, led by Ari Sadanandom. They investigate the role of the SnRK1 protein kinase, which is a key enzyme for modulating the plant stress response. This paper adds detail to the cellular mechanisms that regulate SnRK1 and they show that SnRK1 is SUMOylated by the SIZ1 E3 SUMO ligase. SnRK1 is ubiquitinated and degraded in a SIZ1-dependent manner that is lacking in siz1 mutants. Interestingly only active SnRK1 is degraded as the inactive SnRK1 protein is stable but can be easily degraded upon SUMOylation. Finally they show that SnRK1 is involved in a negative feedback loop wherein it controls its own SUMOylation and degradation that, in wildtype cells, prevents a potentially detrimental stress response.

Fuchs R, Kopischke M, Klapprodt C, Hause G, Meyer AJ, Schwarzländer M, Fricker MD, Lipka V (2015) Immobilized subpopulations of leaf epidermal mitochondria mediate PEN2-dependent pathogen entry control in Arabidopsis. Plant Cell

Mark Fricker (Oxford) is the UK research lead on this study that investigates the role of the atypical myrosinase PEN2 in the response to pathogen attack. PEN2 is targeted to both peroxisomes and mitochondria and can also form homo-oligomer complexes. PEN2 localised to mitochondria are immobilized following fungal invasion and this accompanies mitochondrial arrest. The substrate for PEN2 is produced by the cytochrome P450 monooxygenase CYP81F2, which is localized to the ER and moves toward immobilized mitochondria. The critical function of PEN2 in that organelle was confirmed by the result that showed exclusive mitochondria targeting could rescue pen2 mutant phenotypes. The authors show by live-cell imaging that arrested mitochondria in domains of plant-microbe interaction exhibit a pathogen-induced redox imbalance that may lead to production of intracellular signals.

Ortiz-Ramírez C, Hernandez-Coronado M, Thamm A, Catarino B, Wang M, Dolan L, Feijó JA, Becker JD (2015) A transcriptome atlas of Physcomitrella patens provides insights into the evolution and development of land plants. Mol Plant.

Liam Dolan (Oxford) is an author on this study that is led from Portugal and is an investigation of the transcriptome of the model moss Physcomitrella patens throughout its life cycle. They also compare transcriptomes from P.patens and Arabidopsis, allowing the authors to identify transcription factors that are expressed in tip growing cells. Interestingly they identified differences in expression patterns that might account for the differences between tip growth in moss and the Arabidopsis root hairs, an area that is the expertise of the Dolan lab.

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January 2016

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