Arabidopsis Research Roundup: August 27th

The Arabdopsis Research Roundup broadens its remit this week. As well as including three original research papers, which look at casparian strip formation, light and hormone signaling, we also highlight an important viewpoint article that aims to set standards for synthetic biology parts. In addition we include a meeting report from a plant synthetic biology summer school and interviews with plant scientists at the JIC, Caroline Dean and Anne Osbourn.

Kamiya T, Borghi M, Wang P, Danku JM, Kalmbach L, Hosmani PS, Naseer S, Fujiwara T, Geldner N, Salt DE (2015) The MYB36 transcription factor orchestrates Casparian strip formation Proc Natl Acad Sci USA Open Access

GARNet Advisory Board Chairman David Salt (Aberdeen) leads this international collaboration that looks at the (relatively) poorly understood Casparian strip (CS), a lignin-based filter that lies in root endodermal cells. Formation of the CS is initiated by Casparian strip domain proteins (CASPs) that recruit other proteins, which begin the process of lignin deposition. In this study the authors look upstream this process and identify the transcription factor MYB36 that directly regulates expression of CASPs and is essential for CS formation. Ectopic expression of MYB36 in root cortical tissues is sufficient to stimulate expression of CASP1-GFP and subsequent deposit a CS-like structure in the cell wall of cortex cells. These results have implications for the design of future experiments that aim to control how nutrients are taken up by the plant as even though myb36 mutants have a ‘root-defect’, they also have changes to their leaf ionome.

Sadanandom A, Ádám É, Orosa B, Viczián A, Klose C, Zhang C, Josse EM, Kozma-Bognár L, Nagy F (2015) SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana Proc Natl Acad Sci USA Open Access

Ari Sadanandom (Durham) and Ferenc Nagy (Edinburgh) are the leaders of this study that investigates the precise function of the PhyB photoreceptor protein. PhyB interacts with a wide range of downstream signaling partners including the PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. The small ubiquitin-like modifier (SUMO) peptide is conjugated to larger proteins to bring about a variety of signaling outcomes. In this case the authors find that SUMO is preferentially attached to the C-term of PhyB under red light conditions, a relationship that occurs in a diurnal pattern. SUMOylation of PhyB prevents interaction with PIF5 whilst the OVERLY TOLERANT TO SALT 1 (OTS1) protein likely de-SUMOlyates PhyB in vivo. Altered levels of PhyB SUMOylation cause distinct light-responsive phenotypes and as such this paper adds another level of regulation to the already complex known network that controls light signaling.

Schuster C, Gaillochet C, Lohmann JU (2015) Arabidopsis HECATE genes function in phytohormone control during gynoecium development Development. Open Access

Christopher Schuster who is now a postdoc based at the Sainsbury lab in Cambridge is the lead author on this investigation into the role of the HECATE (HEC) family of bHLH transcription factors on fruit development in Arabidopsis. During this process HEC proteins are involved in the response to both the phytohormones auxin and cytokinin, the authors proposing that HEC1 plays an essential role in Arabidopsis gynoecium formation.

Patron N et al (2015) Standards for plant synthetic biology: a common syntax for exchange of DNA parts New Phytologist Open Access

Carmichael RE, Boyce A, Matthewman C Patron N (2015) An introduction to synthetic biology in plant systems New Phytologist Open Access

Although not strictly based on Arabdopsis work, there are a couple of articles in New Phytologist that have broad relevance to plant scientists who are interested in plant synthetic biology. In the first of these Nicola Patron (The Sainsbury Laboratory) leads a wide consortium that aims to set parameters for the standardisation of parts in plant synthetic biology. It is hoped that as the principles of synbio are used more widley in the plant sciences that the proposals in this paper will serve as a useful guide to standidise part production. GARNet has recently written a blog post on this topic.
The associated meeting report looks at the use of plant synthetic biology in a teaching context with a synopsis of the ERASynBio summer school hosted by John Innes Centre. In this event, young researchers from a range of backgrounds were introduced to the power and potential of plant synthetic biology through a diverse course of lectures, practical session and group projects.


Vicente C (2015) An interview with Caroline Dean Development Open Access

An interview with Anne Osbourn (2015) New Phytologist <a href="http://dx.doi acheter″ onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘’, ‘ ‘]);” target=”_blank”> Open Access

These are interviews with eminent female plant molecular biologists who both work at the John Innes Centre. Caroline Dean’s lab focuses on the epigenetic mechanisms that regulate vernalisation whilst Anne Osbourn is interested in using synthetic biology approaches to engineer metabolic pathways for the production of novel compounds.

Plant research goes EPIC

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Published on: October 25, 2013
A DNA molecule that is methylated on both strands on the center cytosine. DNA methylation plays an important role for epigenetic gene regulation in development

Early last week I attended the EPIC (Epigenomics of Plants International Consortium) one day symposium on Mapping the Epigenomes of Plants and Animals at the John Innes Centre. Epigenomics is an exciting branch of biology, with active, cutting-edge research ongoing in plants, animals and microbes alike.

The EPIC Planning Committee aim to crack and control the ‘second code’ of biology (they overview the field and their plans in a 2012 open access Plant Cell paper). A major step toward this ambitious goal is the CoGe Epigenomics Browser, a web-based comparative genomics system that provides access to 20,000 genomes from 15,000 organisms, and users can take advantage of over 30 tools for the analysis, comparison, and visualisation of genomic data from the scale of whole genomes to individual nucleotides. The creators of CoGe, Eric Lyons and Brian Gregory, have worked with iPlant to build a secure and versatile user-data management system, and like iPlant CoGe has a Wiki with extensive tutorials and support pages.

The biggest session at the Symposium was on DNA methylation. Gavin Kelsey, Mary Gehring and Rob Martienssen, who is speaking at GARNet 2014, spoke about the mechanisms of parental imprinting and their impact, which can continue for generations – and I have to say, at this point I wondered how many lab conflicts and frustration-inducing experimental problems are caused by our current lack of understanding about epigenomic effects!

Julie Ahringer and Doris Wagner spoke about their research digging down into the physical properties of epigenomic features and the mechanisms of chromatin regulation. Oliver Stegle and Claude Becker are both working on understanding how genome, transcriptome, epigenome and environment interact to produce a phenotype. Xiaofeng Cao is applying this approach to controlling agricultural traits in rice.

There were a few non-plant science speakers, including Eric Miska who presented his research on piRNAs, which he has shown are vital for maintaining fertility over generations and are also involved in sperm production. Interestingly Blake Meyers has identified phasiRNAs in maize, small RNAs that are involved in sperm production and he suggested they may have convergently evolved to fulfil a similar role as piRNAs.

Image credit: Christoph Boch via Wikimedia Commons. “Details: The picture shows the crystal structure of a short DNA helix with sequence “accgcCGgcgcc”, which is methylated on both strands at the center cytosine.”


Pollen epigenetics

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Published on: October 11, 2012

Biology learned in school and as a first year undergraduate is easily forgotten if it is not relevant to your current research. Today’s highlighted article required me to refresh my memory of plant germ line development, so I included my basic research here.

Highlighted article: Joseph P. Calarco, Filipe Borges, Mark T.A. Donoghue, Frédéric Van Ex, Pauline E. Jullien, Telma Lopes, Rui Gardner, Frédéric Berger, José A. Feijó, Jörg D. Becker and Robert A. Martienssen (2012) Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA. Cell 151:194-205.

Germline biosynthesis: A pollen mother cell undergoes meiosis to make haploid microspores, which unevenly split into a larger vegetative cell and a small generative cell. The generative cell splits symmetrically into two – these are the plant ‘sperm’ cells. Each pollen grain contains two sperm cells, which are surrounded by a vegetative cell. The vegetative nucleus contains completely decondensed heterochromatin, but DNA in generative nuclei is tightly condensed.

The female gametophyte develops from a megaspore mother cell. Both the megaspore mother cell and pollen mother cell are specified from somatic cells in developing flowers.

GFP staining in the two sperm nuclei and vegetative nucleus in the vegetative cell.

Bisulphite sequencing is a DNA sequencing method which determines methylation pattern by treating DNA with sodium bisulphite before sequencing it using a conventional DNA sequencing method. Bisulphite induces the conversion of unmethylated cytosines to uracil, but this is not a perfect technique so unmethylated DNA may be recorded as methylated. Additionally, bisulphite treatment can cause DNA degradation. Sequencing the DNA of interest multiple times, in the case of Calarco et al., anywhere from 7 to 17 times, improves reliability of the method. There is a brief overview of DNA methylation in this post. (more…)

Summary for non-specialists: Science paper on epigenetics

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Published on: June 21, 2012

One of the things I wanted to do on this blog was to highlight recent plant science journal articles, and when I found back-to-back papers on Arabidopsis research in Science I thought they would be a good place to start.

But when I started to read, I realised the obvious – my cell wall biochemistry background will be no help at all when trying to understand other areas of plant science research. But I still want to highlight high-impact articles like this on the blog, so I decided to have a Summary for non-specialists series. Please feel free to comment if I’ve got something horribly wrong, and of course if anyone would like to provide a Summary by a Specialist that would be great!

Highlighted article

Qian et al., June 2012. A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis. Science 336: 1445-1447

Prior to this research, little was known about the regulation of DNA methylation, or how DNA and histone modifications were related. Here, Qian et al. define a process in which histone modification is an essential part of DNA methylation. This research opens the door to deeper understanding of the regulation and mechanism of DNA modification, and possible manipulation of epigenetic mechanisms.


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