Arabidopsis Research Roundup: July 30th

Two broad topics dominant the studies featured in this weeks Arabidopsis Research Roundup. Environmental and hormonal factors that control different types of ‘dormancy’ are presented in studies from the labs of Caroline Dean (JIC) and Ian Graham (York). Elsewhere two Sainsbury lab (Norwich) led studies investigate different aspects of the interaction between plants and bacterial pathogens. Finally Colin Turnbull from Imperial College is involved in an interesting assessment of cytokinin concentrations across the root tip.

Duncan S, Holm S, Questa J, Irwin J, Grant A, Dean C (2015) Seasonal shift in timing of vernalization as an adaptation to extreme winter Elife. http://dx.doi.org/10.7554/eLife.06620

Caroline Dean (JIC) again publishes in the open access journal eLife as her lab continues to investigate the precise detail of the vernalisation response. This response shows natural variation that is dependent on the geographic distribution of Arabidopsis ecotypes. Plants collected from northern latitudes showed maximum vernalisaton at 8oC, both at the level of flowering time and FLC chromatin silencing. The vernalisation response was measured both in controlled and field conditions and all Northern ecotypes were importantly shown to vernalise prior to snowfall, which would allow flowering immediately after thawing. These findings have important implications for models aimed at predicting the affect of climate change on flowering time.

Ibarra SE1, Tognacca RS1, Dave A2, Graham IA2, Sánchez RA1, Botto JF (2015) Molecular mechanisms underlying the entrance in secondary dormancy of Arabidopsis seeds Plant Cell Environ http://dx.doi.org/10.1111/pce.12607

Ian Graham is the leader of the Centre for Novel Agricultural Products (CNAP) at the University of York and contributes to this Argentinian-led study that looks into the molecular factors that underlie secondary dormancy in Arabidopsis seeds. They show that this process involves changes in the content and sensitivity to GA (but not ABA) that requires the activity of the RGL2 protein acting through ABI5. A wide geographical study then perhaps unsurprisingly showed that temperature is also an important variable influencing the induction of secondary dormancy

Lee D, Bourdais G, Yu G, Robatzek S, Coaker G (2015) Phosphorylation of the Plant Immune Regulator RPM1-INTERACTING PROTEIN4 Enhances Plant Plasma Membrane H+-ATPase Activity and Inhibits Flagellin-Triggered Immune Responses in Arabidopsis Plant Cell http://dx.doi.org/10.1105/tpc.114.132308

Silke Robatek (TSL) is the UK lead on this collaboration with UC-Davis that looks at phosphorylation of RPM1-INTERACTING PROTEIN4 (RIN4) in a range of Arabidopsis genotypes that are suspectible to infection. Flexibility of the RIN4 protein is affected by phosphorylation and this causes enhanced suspectibility coincident with increasing plasma membrane H+-ATPase activity. The expression of the AHA1 ATPase is high in guard cells and therefore linked to stomatal opening. As such bacterial infection works to phosphorylate RIN4 that in turn increases the chance of bacterial entry.

Pfeilmeier S, Saur IM, Rathjen JP, Zipfel C, Malone JG (2015) High levels of cyclic-di-GMP in plant-associated Pseudomonas correlate with evasion of plant immunity Mol Plant Pathology http://dx.doi.org/10.1111/mpp.12297

GARNet Advisory Board Member Cyril Zipfel (TSL) and Jacob Malone (JIC) investigate the response to pathogen/microbe-associated molecular patterns (PAMPs/MAMPs) by the plant innate immune system. The resulting pattern-triggered immunity (PTI) fends off pathogen attack by recognition of bacterial flagellin by, amongst others, the FLAGELLIN SENSING2 (FLS2) protein. In this study the authors focus on the bacterial side of the response and show that cyclic-di-GMP is involved in the evasion of PTI, although this also reduces virulence, likely due to reduced flagellar motility. This results in a trade off for the bacteria in which it is not recognised as readily by plant yet isn’t as virulent.

Antoniadi I, Plačková L, Simonovik B, Doležal K, Turnbull C, Ljung K, Novák O (2015) Cell-Type-Specific Cytokinin Distribution within the Arabidopsis Primary Root Apex Plant Cell http://dx.doi.org/10.1105/tpc.15.00176

Colin Turnbull (Imperial College) is a contributor to this Swedish-Czech collaboration that measures cytokinin concentrations in root cell files isolated by FACS and analysed by MS. The authors show a gradient of cytokinin across the root tip with maximum concentrations in the lateral root cap, columnella and QC cells. As these are also areas of high auxin concentration, the authors suggest that this implies that interactions between the two hormone groups are cell type specific.

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:
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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.

Plant Doctors at the Big Bang Fair

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Published on: March 19, 2014

BigBang cover2

On Friday I went to the NEC in Birmingham to join an intrepid team of plant scientists running activities on an exhibit at the free national science, technology and engineering event the Big Bang Fair. The stand was organised and funded by the British Society of Plant Pathology and the John Innes Centre.

The theme of the exhibit was Plant Doctors. Visitors learned about plant diseases and were encouraged to think about a world without plant doctors – what effects would uncontrolled plant diseases have on our air quality and food supply?

There were four activities on the stand, aimed at different age groups.

The main event was the Plant Doctors activity, where children and young people could don a white coat and clipboard and learn to diagnose a bacterial, fungal or viral plant disease. In my experience the particularly gruesome crown gall tumour (just like the black death!) went down well, but some groups were fascinated by the spores on the bean rust pustules (little mushrooms), which we showed them down the microscope.

At the Polling Station, adults and young people discussed the benefits and drawbacks of bio-control, pesticides and GM approaches to controlling plant pathogens. Older Plant Doctors were also invited to vote on how best to treat the plant diseases. I didn’t spend much time on this activity, but it seemed to keep some groups very engaged. It was certainly an effective way of talking about the importance of innovation in plant science. (more…)

Ash Dieback News

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Published on: February 21, 2013

 

This video is an introduction to a series of filmed talks from the Forestry Commission Plant Health Conference. It introduces the ash dieback problem nicely and places it in a wider context. A number of experts give their opinions on how to approach combatting the disease.

Another new tree health resource is the UKPSF’s Ash Dieback web resource, which was launched this week. Mimi Tanimoto, Executive Officer of the UKPSF, said, “Speaking to scientists who wanted to do something to help combat ash dieback, I found a recurring problem that they were unsure of what else was happening. It was clear that by joining up the various projects we could better tackle the disease.” The website will be updated regularly with news, and it is possible to sign up on the site to receive these updates via email. Anyone who has news that they would like added to the site can contact Mimi at mimitanimoto@societyofbiology.org.

The final piece of ash dieback news is that the Open Ash Dieback project, which crowdsources genome analysis of ash trees and the fungal pathogen Chalara fraxinea,published their first paper last week. Crowdsourcing genomic analyses of ash and ash dieback – power to the people by researchers from several UK universities, lead by two groups at the Sainsbury Laboratory, was published in GigaScience 2:2 doi:10.1186/2047-217X-2-2.

Ash trees and human health

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Published on: January 24, 2013
A lone ash tree in Worcestershire

I have to admit that as a plant scientist plugged into the major social media networks that when I was inundated with articles and posts about ash dieback (Chalara fraxineai) in December, I got a bit fed up with it. Of course I appreciate all species have intrinsic value and it will be sad if Britain loses its ash trees – but I have no emotional attachment to ash trees, and pathogens are a fact of life. British countryside is managed land, so with effective management other trees will fill the gaps. However, a paper published in the February issue of American Journal of Preventive Medicine (Donovan et al., 2013) suggests the health effects on humans of losing trees are significant, and that serious loss of ash trees in the UK could have consequences beyond the financial burden on the forestry industry and the short-term loss of trees. 

Adult emerald ash borer on a penny

The research paper is an analysis of the effects of emerald ash borer (Agrilus planipennis) damage to North American ash trees. Emerald ash borer is a green beetle native to Asia, and was introduced to North America in 2002. It causes significant damage to all North American ash species and an infestation can kill a mature tree within four years. For this study, Donovan et al. looked at human mortality data from 1296 counties across the 15 states where there were confirmed emerald ash borer infestations in 2010. (more…)

Molecular Plant Pathology’s Top Ten

Keeping with last week’s plant pathology theme, I thought I’d highlight a paper that came out in the spring in case any plant pathologists missed it. This may also help people in other fields of plant science out there who might need to hold their own in a pathology-based conversation occasionally. In April 2012, Molecular Plant Pathology published ‘The top 10 fungal pathogens in molecular plant pathology,’ as voted for by 495 readers of the journal.

Quesadillas made with corn infected with Ustilago maydis, which is called huitacoche.

The pathogens chosen are:

  1. Magnaporthe oryzae, the cause of rice blast disease.
  2. Botrytis cinerea, also known as grey mold – probably the cause of the mold on the strawberries in the back of the fridge that you bought when they were offer.
  3. Puccinia spp., the cause of an unpleasant range of rust diseases that occur on wheat.
  4. Fusarium graminearum, a cereal pathogen commonly known variously as head blight, ear blight, or, delightfully, head scab. Infected grain can be poisonous.
  5. Fusarium oxysporum, a ubiquitous soil-borne pathogen that can infect many species, including important fruit species, and humans.
  6. Blumeria graminis, powdery mildew, which infects wheat and barley.
  7. Mycosphaerella graminicola is also called Septoria tritici and causes blotch disease in wheat.
  8. Colletotrichum spp. can infect a large range of crops, and latent infections can destroy stores of fruits post-harvest.
  9. Ustilago maydis, or corn smut, is actually cultured on corn cobs by farmers in Mexico, where the infected corn is called huitacoche and is a common recipe ingredient.
  10. Melampsora lini, or flax rust, the classic model plant pathogen.

The paper gives a ‘resume’ of each one, written by an expert in that particular species. Is your favourite pathogen missing? What other ‘Top 10’ would be interesting to put together?

Paper: DEAN, R., VAN KAN, J. A. L., PRETORIUS, Z. A., HAMMOND-KOSACK, K. E., DI PIETRO, A., SPANU, P. D., RUDD, J. J., DICKMAN, M., KAHMANN, R., ELLIS, J. and FOSTER, G. D. (2012), The Top 10 fungal pathogens in molecular plant pathology. Molecular Plant Pathology, 13: 414–430. doi: 10.1111/j.1364-3703.2011.00783.x

Teaching resources: This is an exercise easily recreated in a tutorial group or classroom. Groups of students could each make a pitch for their plant pathogen (or crop species, or organelle, etc …) and the whole group would vote for which one deserves the ‘top’ spot.

Image credit: Lesley Téllez, via her blog The Mija Chronicles

Systems of plant defence

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Published on: November 8, 2012
Arabidopsis leaf cells, stained to visualise the cell wall and Botrytis cinerea mycelia

Today’s highlighted paper demonstrates the scale of the pathogen response in greater detail than has been published previously. Windram et al. (2012) profiled gene expression in Arabidopsis thaliana leaves every two hours after infection with Botrytis cinerea, until the fungus was truly established 48 hours after infection.

On the whole, until now research into the pathogen response has been at the pathway-level. Many details are known about the plant pathogen response, for example it is possible to identify loci responsible for resistance, as highlighted on this blog last week, and the intricacies of the oxidative burst are being discovered. When we understand these kinds of details, it is possible to make aphid-repellant crops, and harness the TALE tools used by Xanthomonas spp. to make disease resistant rice. On the other hand, they are just details – a close-up, zoomed in fraction of the whole, and broadly speaking it is luck if a piece of research provides anything of commercial worth.

A systems biology approach allows us to see the whole picture rather than the details of a close-up. From the data in Windram et al., we now know that a third of the Arabidopsis genome is differentially expressed in leaves infected with Botrytis compared to mock-inoculated controls. This represents a huge chunk of defence-related pathways, not previously studied, which could be affected by any attempts to improve pathogen resistance in plants.

This experiment was a timecourse, which allowed the team to record the timings of defence response pathways to two-hour time slots, like ethylene synthesis at 14 hours and response to jasmonic acid at 16 hours post-infection. Additionally, it showed that pathways including translation, photosynthesis, and protein phosphorylation were all down-regulated, and the order and timing in which they occurred. The ability to assign each process a time is important for modelling and predicting regulatory mechanisms.  (more…)

The genetics of broad-spectrum resistance

Downy mildew infection of Arabidopsis thaliana seedlings

Highlighted article: Dmitry Lapin, Rhonda C. Meyer, Hideki Takahashi, Ulrike Bechtold, Guido Van den Ackerveken (2012) Broad-spectrum resistance of Arabidopsis C24 to downy mildew is mediated by different combinations of isolate-specific loci. New Phytologist DOI: 10.1111/j.1469-8137.2012.04344.x

It is a mark of how effective plant immune systems are that most bacteria, fungi, and viruses do not affect plants at all either because plant tissues are not suitable for them to live in, or they are fended off. Of course there are pathogens that are compatible with plants – and within species that share compatibility, there are pockets of resistance. Some sub-groups are resistant to specific pathogen isolates, and this is caused by dominant resistant genes. A much broader, more complicated, and less common form of resistance occurs when a particular accession is resistant to a whole pathogen species, or several species. This is broad-spectrum resistance, and it can be caused by a simple dominant gene or multiple genes. Natural broad-spectrum resistance is not simple to transfer from its origin to a commercial crop because it can come from a complex set of genes which are not necessarily all dominant. (more…)

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