Arabidopsis Research Roundup: Sept 29th

This weeks Arabidopsis Research Roundup includes papers, from Glasgow and Oxford, that look at a plants response to different abiotic stresses and uncover control mechanisms that might have potential as targets for future genetic modification or gene-editing strategies. In addition there is a study from Leeds that uncovers a novel molecular mechanism in the DNA repair pathway and finally an international group of researchers with a UK lead at Kings College use infrared microspectroscopy to investigate internal cellular structures

Ji H, Wang Y, Cloix C, Li K, Jenkins GI, Wang S, Shang Z, Shi Y, Yang S, Li X (2015) The Arabidopsis RCC1 Family Protein TCF1 Regulates Freezing Tolerance and Cold Acclimation through Modulating Lignin Biosynthesis PLoS Genetics 11(9):e1005471

Gareth Jenkins (Glasgow) is the UK lead representative on this Chinese-led study into the role of the ‘Tolerant to Chilling and Freezing 1’ (TCF1) protein. This protein is induced by the cold to move to the nucleus where it interacts with histones H3 and H4, specifically at the BLUE-COPPER-BINDING PROTEIN (BCB) locus, which is involved in lignin biosynthesis. Loss of TCF1 causes changes in the positive histone mark H3K4me2 as well as the negative mark H3K27me3, resulting in reduced lignin content and enhanced freezing tolerance. This growth phenotype was recapitulated in other mutants that have reduced level of lignin. Therefore the authors suggest that TCF controls a CBF-independent signaling pathway that reacts to cold conditions by causing cell wall remodeling. In tcf mutants this pathway does not function correctly and the plants are more tolerant to freezing conditions. This marks either TCF or the genes downstream of it as potential targets for genetic modification to develop cold-resistant plants. The associated figure is taken from PLoS Genetics.


Ling Q1, Jarvis P (2015) Regulation of Chloroplast Protein Import by the Ubiquitin E3 Ligase SP1 Is Important for Stress Tolerance in Plants Current Biology.

Paul Jarvis (Oxford) is an expert on the mechanisms that control protein import into the chloroplast and this study looks at the interaction of the TOC translocon apparatus with ubiquitin-proteasome system. The chloroplast envelope-localised E3 ubiquitin-ligase SUPPRESSOR OF PPI1 LOCUS1 (SP1) was previously known to regulate levels of TOC and so control protein import and impact the composition of the chloroplast proteome. This study is expanded to show that SP1 plays an important role in the response to abiotic stress with sp1 mutants being hypersensitive to salt, osmotic, and oxidative stresses whereas the opposite is true in SP1 OX plants. They uncover the molecular mechanism to this response by showing SP1 facilitates the depletion of the TOC apparatus, subsequently reducing the import of photosynthetic apparatus components which attenuates photosynthesis and reduced the production of potentially damaging reactive compounds in the chloroplast. The authors show that chloroplast protein import is responsive to environmental cues and this modulation of this process might open up new avenues of research for improving stress tolerance in crops.

Waterworth WM, Drury GE, Blundell-Hunter G, West CE (2015) Arabidopsis TAF1 is an MRE11-interacting protein required for resistance to genotoxic stress and viability of the male gametophyte The Plant Journal

Christopher West (Leeds) is the research lead on this investigation into the essential function of double strand breaks (DSBs) during recombination. These DSBs are repaired by the endonuclease MRE11 and this work demonstrates an interaction with the histone acetyltransferase TAF1, which is an essential gene in Arabidopsis. The remainder of the paper uses genetic and phenotypic analysis to show that TAF1 is important for gamete viability in an effect that is dosage dependent. Taf mutants are more sensitive to genotoxic stresses thus showing that the TAF1 protein has a specific role in the DNA damage response. This provides new insights into the molecular mechanisms of the DNA damage response in plants.

Warren FJ , Perston BB, Galindez-Najera SP, Edwards CH, Powell PO, Mandalari G, Campbell GM, Butterworth PJ, Ellis PR (2015) Infrared microspectroscopic imaging of plant tissues: spectral visualisation of wheat kernel and Arabidopsis leaf microstructure. Plant Journal

This international study was led by <a href=" recherche cialis.aspx” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘’, ‘Peter Ellis’]);” target=”_blank”>Peter Ellis (Kings College) and includes a variety of labs not usually connected with Arabidopsis work but rather are interested in the interaction between the plant cell wall and the human gut. They used Infrared microspectroscopy as a tool to investigate the microstructure of wheat kernels and Arabidopsis leaves. This technique was able to discern structures such as starch granules and protein bodies within cells. Stimulated digestion on the wheat tissues showed that digestion promotes a loss of starch as might be predicted. This article might be of interest to plant scientists who are interested in use of infrared spectroscopy.

Arabidopsis Research Roundup: July 20th

There is a bumper crop of publications in high quality journals in this weeks UK Arabidopsis Research Roundup, including manuscripts in PNAS, Nature Communications, PLoS Genetics , PloS One and Plant Physiology. Malcolm Bennett, Alex Webb and Anthony Hall lead a major collaborative effort that links the circadian clock with lateral root formation whilst Ottoline Leyser (SLCU) and Mike Bevan (JIC) participate in a similarly broad consortium in a study linking organ size and MAPK signaling. Liam Dolan’s group from Oxford looks at mechanisms of tip-growth across the plant kingdoms whilst elsewhere three members of faculty at the University of Birmingham are involved in two papers looking at the regulation of meiosis. Finally there are two US-led studies that include significant contributions from UK-based researchers, including Matthew Jones from the University of Essex.


Voß U, Wilson MH, Kenobi K, Gould PD, Robertson FC, Peer WA, Lucas M, Swarup K, Casimiro I, Holman TJ, Wells DM, Péret B, Goh T, Fukaki H, Hodgman TC, Laplaze L, Halliday KJ, Ljung K, Murphy AS, Hall AJ, Webb AA, Bennett MJ (2015) The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana Nature Communication 6:7641.

Once again Malcolm Bennett (CPIB) leads a multi-Institute collaboration that includes Alex Webb (Cambridge) and current GARNet board member Anthony Hall (Liverpool). This is also an extremely international effect with groups from the UK, USA, Sweden, Japan, Spain and France. The science looks at lateral root stems cells and how the circadian clock is rephased during LR emergence. They show that the clock controls auxin levels and auxin-related genes. The conclusion is that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence and adds to a growing portfolio of evidence that suggest the circadian clock might act in a cell autonomous manner. Anthony Hall, James Locke and Peter Gould currently have a grant that is looking at this phenomenon in Arabidopsis root cells.


Johnson KL, Ramm S, Kappel C, Ward S, Leyser O, Sakamoto T, Kurata T, Bevan MW, Lenhard M (2015) The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis PLoS One.10(7):e0131103.

Ottoline Leyser, Sally Ward (Sainsbury lab, Cambridge) and Mike Bevan (JIC) are the UK contributors to this joint UK-German-Japanese-Australian collaboration. This study follows a screen for plants with reduced organ size and introduces a novel allele of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5), named Tinkerbell (tink). This mutation reveals that IBR5 is a novel regulator of organ size by changing the growth rate in petals and leaves although this occurs independent of the previously characterised KLU pathway. The authors use microarray data to suggest an additional role for TINK/IBR5 during male gametophyte development. Ultimately they conclude that IBR5 might influence organ size through auxin and TCP growth regulatory pathways.


Tam TH, Catarino B, Dolan L (2015) Conserved regulatory mechanism controls the development of cells with rooting functions in land plants Proc Natl Acad Sci U S A.

Liam Dolan’s lab at the University of Oxford is a world leader in the study of root hair development. Previously it has been shown the group XI basic helix-loop-helix (bHLH) transcription factor (LOTUS JAPONICUS ROOTHAIRLESS1-LIKE (LRL) regulates root hair growth in Arabidopsis, Lotus or rice. This study investigates the equivalent proteins in the moss Phycomitrella patens and show that they are involved in an auxin signaling pathway that promotes cell outgrowth albeit via a different set of signaling intermediates. Overall the authors show that a core auxin network that supports cellular ‘tip-growth’ exists throughout land plant lineages even though the specificity of this signaling has diverged over the course of the ~420million years that separates angiosperms and mosses.


Varas J, Sánchez-Morán E, Copenhaver GP, Santos JL, Pradillo M (2015) Analysis of the Relationships between DNA Double-Strand Breaks, Synaptonemal Complex and Crossovers Using the Atfas1-4 Mutant. PLoS Genet.11(7): e1005301.

The work led by Monica Pradillo at the University of Madrid includes a contribution from Eugenio Sanchez-Moran from the University of Birmingham. This work focuses on the hetero-trimeric Chromatin Assembly Factor 1 (CAF-1), which is a histone chaperone that assembles acetylated histones H3/H4 onto newly synthesized DNA. In Arabidopsis the CAF1 complex is composed of the FAS1, FAS2 and MSI1 proteins. Atfas1 mutant plants are less fertility, have a higher number of double stranded breaks (DSB) and show a higher gene conversion frequency. The authors investigate how DSBs can influence meiotic recombination and synaptonemal complex (SC) formation by genetic analysis of Atfas1-containing double mutants. Ultimately their experiments provide new insights into the relationships between different recombinase proteins in Arabidopsis. Overall an increase in the number of DSBs does not translate to an increase in the number of crossovers (COs) but instead in a higher GC frequency. The authors provide different theories to explain this mechanism, including the possible existence of CO homeostasis in plants.


Lambing C, Osman K, Nuntasoontorn K, West A, Higgins JD, Copenhaver GP, Yang J, Armstrong SJ, Mechtler K, Roitinger E, Franklin FC (2015) Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers PLoS Genetics 11(7):e1005372

The University of Birmingham is the lead Instiution in this study that also investigates regulation of meiosis. The groups of Chris Franklin and Sue Armstrong collaborate with US and Austrian partners to study the organization of meiotic chromosomes during prophase I. Using structured illumination microscopy (SIM) they show that dynamic changes in chromosome axis is coincident with synaptonemal complex (SC) formation and depletion of the ASY1 protein, which requires the function of the PCH2 ATPase. Using a pch2 mutant the authors are able to tease apart different aspects of ‘crossover’ (CO) biology and that the pch2 defect occurs precisely during CO maturation, not during designation. In addition, CO distribution is also affected in some chromosome regions showing that failure to deplete ASY1 can result in downstream events that include disruption of CO patterning.


Jones MA, Hu W, Litthauer S, Lagarias JC, Harmer S (2015) A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light Plant Physiology.

Matthew Jones (University of Essex) is the primary author of this work that comes from a collaboration from his time in the lab of Stacey Harmer in UC Davis. Since 2012 Matthew has been a lecturer at the University of Essex where he continues with work of this nature. In this study they introduce a constitutively active allele of the PHYB photoreceptor that is able to phenoopy red-light input into the circadian clock. In these mutants the pace of the clock is insensitive to light-intensity and this response is dependant on its PHYB nuclear localisation. Finally they show that fine tuning of PHYB signalling requires PHYC and overall they conclude that nuclear phytocrome signalling is necessary for sustaining clock function under red light.


Chakravorty D, Gookin TE, Milner M, Yu Y, Assmann SM (2015) Extra-Large G proteins (XLGs) expand the repertoire of subunits in Arabidopsis heterotrimeric G protein signalling Plant Physiol.

Sally Assman from Penn State University leads this study that includes a contribution from Matthew Milner who now works at NIAB. The number of proposed G protein subunits is greatly reduced in diploid plant genomes yet this study shows that a family of Arabidopsis GPA-related proteins (XLG1-3) can increase the repertoire of potential G proteins interactions by interacting with beta and gamma subunits. The authors propose they have uncovered a new plant-specific paradigm in cell signaling.

Multi-scale Biology Meeting.

What is Multi-scale Biology?

That was the overriding question that occupied attendees of the inaugural meeting of the Multi-scale Biology Network, held at the University of Nottingham on June 1st 2015. This newly funded BBSRC network brought together biologists, physicists, engineers, and the funding bodies (amongst others) for this meeting that aimed to set the agenda for this area of future collaboration. Storify of the meeting.

Those who had also been involved in the genesis of synthetic biology policy might have felt a touch of deja-vu over the questions being asked at this meeting. However whereas the term ‘synthetic biology’ might have remained opaque after those early meetings, the feeling at the end of this day was that good progress had been made into an understanding of what this network might achieve.

Although there were <a href="" onclick="_gaq.push(['_trackEvent', 'outbound-article', 'http://www cialis 20mg en’, ‘speakers from a range of biological disciplines’]);” target=”_blank”>speakers from a range of biological disciplines there was no requirement for forced interactions between different research areas. Instead there was a sense of ‘wondering what can be learnt‘ when for example, plant scientists talked to neurobiologists…

The meeting was kicked off by Professor Markus Owen from the Nottingham Maths department and the agenda had been clearly designed to encourage significant amounts of discussion, be it during the lecture period or over an extended lunch in which attendees split into small groups to discuss challenges in MSB.

Many of the attendees were involved in some form of systems biology so the sense was that MSB comes as the natural extension of that area of research. Instead of looking at a single network, how should researchers extend their thinking to include how these networks interact at different scales…..without losing the quality of analytic data?

Professor Alfonso Martinez-Arias (Cambridge) led the first discussion and made the important point that even though we now have enormous amounts of data, what is it we actually want to learn?….and is focusing on that type of question compatible with current necessity for publication in high quality journals?

Immediately after lunch Professor Carole Goble introduced a new ERASysApp network (FAIRdom) in which she is involved that aims to ensure that systems biology projects make their data, operating procedures and models, Findable, Accessible, Interoperable and Reusable (FAIR). This was a timely reminder that it is very important to produce data that is reusable by the community so that people aren’t reinventing the wheel in each experiment. In 2016 GARNet will be hosting a meeting with the Exeter Centre for the Study of Life Sciences that will address issues surrounding data reuse. Details to follow later in 2015!

Toward the end of the day Professor Martin Howard from the John Innes Centre led the final discussion that attempted to coalesce the thoughts of attendees. One suggestion was for biologists to act ‘like engineers’ and to use ‘dirty tricks’ as to get tasks completed. Understanding the details can come later…. getting the job done is most important….. whatever the job is that needs to be done! It was also discussed that coming to any ‘effective theory’ of biology is almost impossible given the unpredictable nature of the field.

The results of group discussions!

The results of group discussions!

Overall it seems that making any decisions about how multi-scale biology projects can be implemented will depend on the funding environment. To that end Michael Ward from the EPSRC stressed that mathematical biology is important for mathematical science funding and urged attendees not to be put off from looking in their direction. Ceri Lyn-Adams from the BBSRC informed the group that although there wasn’t any money specifically ring-fenced for MSB, they welcome applications in this area under existing mechanisms.  What was clear is that MSB and systems biology remain in the forefront of BBSRC funding strategy!

By it’s very nature MSB will require large projects that might bring together a few responsive mode-size projects under a single umbrella. Hopefully new researchers will be able to be involved in this type of project and the money doesn’t all go to large established groups.

Plant Scientists were well represented at the meeting most notably by Martin Howard, Malcolm Bennett and Leah Band, who gave the final talk of the day. The multi-scale nature of plant biology was highlighted in this more than any other talk, as Leah discussed biology at the organismal, tissue, network, cellular and enzyme level. Her work builds the prior knowledge of GA transport and biosynthesis to make mathematical models to predict tissue expansion.
Multi-scale Plant Biology

Importantly for the GARNet community, the take home message from the meeting was that plant scientists will play a major role in the future of multi-scale biology so once the funding opportunities are revealed they should not be reticent in submitting bids.

Great British Success in ERA-CAPS

The ERA-CAPS funding call was a major EU initiative that was focused on plant sciences. Recently the second set of successfully funded projects were announced, even though the funding levels have not been confirmed. Amongst these twelve successful bids, eight feature UK plant scientists (including four from the JIC). These successful projects are highlighted below:
Project Name: DesignStarch, Designing starch: harnessing carbohydrate polymer synthesis in plants

The UK representative Rob Field is a biochemist based at the John Innes Centre. The objective of this project is to ‘gain a profound understanding of the regulation and control of the biophysical and biochemical processes involved in the formation of the complex polymeric structure that is the starch granule’, which will involve in vitro analysis of the enzymology of starch formation with the ultimate aim of transferring their findings back into plants.

EfectaWheat: An Effector- and Genomics-Assisted Pipeline for Necrotrophic Pathogen Resistance Breeding in Wheat

James Cockram (NIAB) is the project leader on this grant that proposes to investigate the economically important wheat leaf spot group (LSG) of necrotrophic pathogens. The project will use a range of techniques such as high-density genotyping, pathogen re-sequencing and advanced virulence diagnosis to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions across Europe.

EVOREPRO: Evolution of Sexual Reproduction in Plants

Both David Twell (Leicester) and Jose Gutierrez-Marcos (Warwick) are included in this seven-group consortium that aims to investigate the origin of the mechanisms that predate double fertilization in plants. The project will take a comparative gene expression-based approach to investigate gametogenesis across Marchantia, Physcomitrella, Amborella, Arabidopsis and a range of crop species. The expected findings will allow the identification of specific mechanisms that are targeted by environmental stresses during sexual reproduction in crops and will assist in the selection of stress-resistant cultivars.

INTREPID: Investigating Triticeae Epigenomes for Domestication

GARNet advisory board member Anthony Hall (Liverpool) leads this group which includes long time collaborator Mike Bevan (JIC). This project will look at variations in the epigenome across eight diverse wheat lines with the aim of determined how epigenetic marks are re-set and stabilized during the formation of new wheat hybrids and how they might influence gene expression.

MAQBAT: Mechanistic Analysis of Quantitative Disease Resistance in Brassicas by Associative Transcriptomics

John Innes Centre scientist Chris Ridout leads this six PI consortium that will look at pathogen resistance in Brassica napus, where diseases are a major limiting factor in growth success. Almost 200 lines of B.napus will be screened against a range of specific and general pathogens in the aim of discovering important disease resistance loci. One proposed aspect of the work will look at the role of glucosinolates in both disease resistace and seed quality. The project also includes UK B.napus expert Bruce Fitt (Hertfordshore).

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Karen Halliday (Edinburgh) leads this three-PI group that will investigate the link between phytochrome signaling and resource allocation in both Arabidopsis and B.rapa. One aim of the project will be to build models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production.

RegulaTomE: Regulating Tomato quality through Expression

Cathie Martin (JIB) leads this largest successful consortium of 8 labs that aim to link transcriptional regulation of metabolic pathways with tomato quality. Loci contributing to abiotic stress tolerance will also be identified toward the combined goals of obtaining more nutritious, stable and sustainable crops. The project will lead to regulatory gene identification (an important advance in terms of fundamental understanding), and provide new tools for metabolic engineering of fruit quality.

SOURSI: Simultaneous manipulation of source and sink metabolism for improved crop yield

Lee Sweetlove (Oxford) leads this group that aims to understand the linkages between source and sink tissues in the assimilation of carbon and nitrogen. The project claims to implement a metabolic engineering strategy of unprecedented scale in plants exploiting the new technique of biolistic combinatorial co-transformation.

The TREE of plant science education

Aurora Levesley is the Project Officer for the Gatsby Plant Science TREE. The TREE grew out of the Gatsby Plant Science Summer Schools as a means of sharing the valuable resources produced for and during the Schools. Here she discusses the value of the TREE’s online lectures, which are the subject of a current New Phytologist paper. 

David Beerling at the Gatsby Plant Science Summer School
David Beerling gives a lecture at the Gatsby Plant Science Summer School. This is one of many lectures that have been edited for interactive online delivery and shared on the Plant Science TREE.

The Plant Science TREE is a free online central repository of plant science educational resources. More than 90 research academics and publishers have contributed over 2000 resources, including online research lectures, research-led lecture slides, practicals, video clips and other resources on topical plant science. It was developed by the University of Leeds with funding from the Gatsby Charitable Foundation, and is currently used by scientists, educators and students from over 320 institutes worldwide.

Many students enter biological sciences courses with little interest in or knowledge of plants, and engaging students with plant science early in their studies is arguably an important step in reversing the decline in uptake of this vulnerable yet strategically important subject linked to food security and other globally important issues. Prof Alison Baker of the Centre for Plant Sciences at the University of Leeds, says of the TREE: “The aim is to put a tool in the hands of educators that will engage students in plant science and research, especially where expertise is becoming limited.”

Our recent study, published in New Phytologist, showed the online research lectures that form a large part of the TREE successfully engage undergraduates with plant science (Levesley et al 2014, New Phytologist Early View).

In this study, undergraduates from four UK universities were provided with links to online research lectures as part of their course. The lectures, filmed at the Gatsby Plant Science summer schools, were given by research leaders but pitched at a level to engage undergraduates and provided a first-hand insight into how discoveries are made and science is carried out.

Not only were the online lectures successful in engaging students with plant science and research in general, but students were unanimous in the opinion that they were a good way to learn about a subject. Interestingly the study also showed that the online viewing experience was comparable to watching the research lectures live.

These online undergraduate research lectures are freely available through the Plant Science TREE. Our study shows they represent a valuable plant science education tool to help lecturers and teachers introduce cutting-edge research examples that address globally relevant applied initiatives – as well as curiosity-driven research – to their students. As such they have the potential to change student attitudes to plant science, engage students in research and are able to reach a large and wide global student audience.

The full reference for the Plant Science TREE paper is: Levesley A, Paxton S, Collins R, Baker A and Knight CD. “Engaging students with plant science: the Plant Science TREE”, New Phytologist, published online ahead of print in June 2014.


A sweet surprise: Revealing new roles for sugars in plants

The fifth post of our Celebrating Basic Plant Science series comes from Mike Haydon, a lecturer at the University of York. He and his research group work on understanding signalling in plants. Here he explains some of his work on integrating sugar metabolism with light signals. You can see more about Mike and his group on his website. The work he discusses below was published in the journal Nature last year (Haydon et al. Nature 502:689-692).



A life based on sugar

Most of us think about sugar every day, be it consciously as we consider our calorie intake, or unconsciously when our brain tells us it’s mealtime. Sugars are among the simplest of carbohydrates and they are the raw material for cellular respiration, which produces energy for almost all living cells. Glucose, a monosaccharide, is the preferred sugar for cellular respiration. Sucrose, most familiar to us as the granulated sugar in our kitchens, is a disaccharide made of glucose and fructose. These, and other simple carbohydrates, are used to build complex carbohydrates such as starch and cellulose in plants, and glycogen and chitin in animals. Sugars are the foundation of cellular metabolism, and produce the wide array of molecules that sustain our carbon-based existence.


The most important process on the planet

Plants, along with algae and some species of bacteria, use photosynthesis to convert carbon dioxide in the air into glucose using energy from sunlight, while producing oxygen as a by-product. Photosynthetic bacteria were responsible for the Great Oxidation Event, which occurred from about 2.5 billion years ago and led to the life-sustaining atmosphere we now live in. Photosynthetic organisms are called autotrophs, because they produce their own sugars to use in cellular metabolism. All other organisms, called heterotrophs, must somehow get their sugars from their environment. For animals, this is ultimately through the plant-based component of their diet. So essentially all the carbon in DSC_0010 smallour bodies was, at some point, converted from carbon dioxide into glucose by photosynthesis. Thus, photosynthesis is probably the most important metabolic process on the planet.

You might think that something so fundamental in biology would be completely understood, and we certainly do know a lot about carbohydrate metabolism. We also know that sugars have functions outside of this basic metabolism. For example in plants they can act as hormones, regulating processes such as cell growth, cell division, flowering time and disease resistance. But there is still a lot we don’t know about how plants regulate carbohydrate metabolism, and sometimes we still find entirely new functions for sugars in biological processes.


How time matters in sugar metabolism (more…)

How do plants remember winter?

Martin Howard is a Professor at the John Innes Centre, one of a small cluster of research institutes in Norwich. In the fourth of our Celebrating Basic Plant Science series, he explains how he uses mathematical modelling to understand how plants remember winter cold and respond to it throughout the year. 

How do plants ‘know’ the correct time to flower? Getting this timing right is vital for reproductive success; flowering in the middle of winter is unlikely to be optimal! Many factors are integrated together to make this critical decision, including the day length.

We have been studying one aspect of this question: How the plant Arabidopsis thaliana perceives and then remembers exposure to winter cold. This fundamental mechanism ensures that flowering doesn’t occur until winter has passed. Interestingly, this memory is quantitative – a longer winter means flowering is faster once it starts (see the image below).  This process is a very nice example of what’s called an epigenetic phenomenon, as the plants store information about winter cold exposure even after the environmental stimulus (cold) has been removed.

So how is this information about cold stored? In Arabidopsis, this is centred on a gene called FLC (Flowering Locus C). When the plant is cold, the FLC gene is turned off. The products of this gene prevent flowering, so turning it off actually stimulates the plant to flower. Over recent years, we have learned a great deal about the operation of FLC and associated genes through genetics and biochemistry, in large part through the work of my experimental collaborator, Caroline Dean. However, despite all this knowledge it was still not clear overall how the epigenetic memory system worked. This was partly due to feedback among the different components, which made arriving at an intuitive understanding a very difficult task. For these reasons, we began to model the dynamics of FLC mathematically in the hope of making sense of these interactions and, we hoped, revealing some underlying simplicity in how the system operated.

Mathematical modelling turned out to be very informative and suggested that FLC gene silencing occurred in an all or nothing fashion inside each cell. (more…)

What makes one species different from another?

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Published on: December 10, 2013

In the third of our series of blog posts Celebrating Basic Plant Science, Catherine Kidner from Edinburgh’s Royal Botanic Garden explains how she pinpoints what makes a species a species. This sheds light onto what drove that species’ evolution. Catherine spoke about her research at a conference earlier in the year – you can see her talk in this video

Catherine Kidner uses genomic data to understand why Begonia like these have evolved into different species

There are likely to be about 9 million species on Earth (not counting bacteria). Each species has traits which define it and allow it to thrive in its niche. My research group at the Royal Botanic Garden in Edinburgh is trying to understand the diversity around us, so we need to know what these traits are and how they contribute to the success, or otherwise, of the species.

There are difficulties with this approach to understanding diversity. For a start, traits we think are important may not be that important to the species concerned. Also, some traits critical to a species’ success might be difficult to measure, for example phosphate uptake by roots; or be seen only on very specific occasions, like response to a particular pathogen.

Using genetics to define differences between species

We get around these problems by looking at genetic differences between species. New sequencing technologies make it relatively quick and easy to sequence the genome of an individual. 

In a typical genome, around 25 000-50 000 genes code for proteins. If we want to know how two species differ we can compare sequences of these protein coding genes and see which types of gene differ the most between species. These changes in gene sequences mean the proteins work differently.

Not all genes are expressed, that is translated into proteins, all the time, and we can see which sets of genes are expressed at particular times and in different organs, like petal or leaf. So when looking at how species differ, we can also look at which genes show the biggest changes in expression level, which would mean one species having more of a particular protein than the other.

Having a list of which genes show sequence changes and which show expression changes is not much help if it’s just a list of genes xzyabc and rst. What really makes this a useful technique are the huge databases which have been built up over the past 20 years. Work in model species such as yeast, Arabidopsis, mouse and Drosophila have determined functions for many genes in typical genomes. We can match the genes in our ‘interesting genes’ lists to sequences from these model organisms to find out that, for example, gene xzy looks like a disease resistance gene, or gene abc looks like a gene that controls root growth rates.

A typical comparative study might highlight hundreds of genes which differ between species, so even with good descriptions of function we still have a lot of data to sift though to find patterns. We can simplify the lists by using GO (Gene Ontology) terms. This is a way of describing what genes do in a very defined way. 


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