A tale of two models

James Lloyd (University of Leeds) was the lead author on last month’s Plant Journal paper on nonsense-mediated mRNA decay, which demonstrated that working on a model plant can sometimes be a hinderance rather than a help. In this guest post he explains how he and his supervisor Brendan Davies overturned widely held assumptions about NMD in plants – by working on moss.

Physcomitrella patens, the model moss, growing on agar.

Plant biology has been greatly advanced by the use of Arabidopsis thaliana as a model. Fantastic community resources, such as mutant collections and numerous genome sequences from natural accessions have aided researchers in all areas of plant sciences. However, A. thaliana is far from perfect. Nonsense-mediated mRNA decay (NMD) is a little heard of pathway to regulate transcript stability and it has recently been shown to be involved in pathogen response in A. thaliana (Rayson et al., 2012).

The mechanism of mRNA decay has largely been worked out in animals and revolves around the phosphorylation of an RNA helicase called UPF1 by a kinase SMG1. However, fungi and A. thaliana both lack the SMG1 kinase, so it has been a mystery how the fungal and plant proteins are phosphorylated. We have recently shown that SMG1 is not animal specific but is an ancient component of the NMD machinery, appearing in the genomes of all plants examined, with the exception of A. thalianaSMG1 is even found in the genome of A. lyrata, a close relative of A. thaliana.

Arabidopsis thaliana, the model plant.

The lack of SMG1 in the genome of A. thaliana meant that we had to use another plant as our model to understand the role of SMG1 in the plant kingdom. Enter moss! Physcomitrella patens is the model moss, with a sequenced genome and a high rate of homologous recombination it is a relatively simple task to identify and delete any gene in the genome. The rate of homologous recombination is much lower in flowering plants than it is in moss, meaning that short (around 1 Kb) of moss genomic DNA from upstream and downstream of a gene of interest can be cloned around an antibiotic selection gene and then transformed into moss cells and a large proportion of antibiotic resistant plants have the gene of interest deleted.

We deleted SMG1 from moss and found that NMD was compromised thus placing plant SMG1 in the NMD pathway (Lloyd and Davies, 2013). Therefore, many plants including crops like rice and maize are likely to rely on SMG1 to control gene expression through NMD. Future research will hopefully reveal why A. thaliana has lost SMG1 and if another kinase has replaced SMG1 in this plant.

A. thaliana has been useful in characterising other components of the NMD pathway in plants, such as UPF1 and understanding the biological role in plants (such as controlling the pathogen response). However, it was limited in helping us understand the NMD pathway of commercially important crops and it was moss to the rescue!

Animal researchers have long used multiple, evolutionarily diverse models, including but not limited to fruit flies, C. elegans, zebrafish, frogs and mice. Despite big differences between invertebrates like fruit flies and vertebrates like humans, a great deal about human biology has been learnt by using these organisms in the lab.

Many important questions cannot be answered by simply studying A. thaliana, big differences in fundamental processes exist between accessions. Therefore, multiple models are needed in plant sciences. Moss is just one plant that can help compliment research in other plant species, using the powerful genetic tool of homologous recombination.

References:

Lloyd JPB and Davies B (2013) SMG1 is an ancient nonsense-mediated mRNA decay effector. The Plant Journal 1365-313X http://dx.doi.org/10.1111/tpj.12329

Rayson S, Arciga-Reyes L, Wootton L, De Torres Zabala M, Truman W, et al. (2012) A Role for Nonsense-Mediated mRNA Decay in Plants: Pathogen Responses Are Induced in Arabidopsis thaliana NMD Mutants. PLoS ONE 7(2): e31917. doi:10.1371/journal.pone.0031917

Images courtesy of James Lloyd. 

Research funding: What strategy is best?

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Published on: November 14, 2013

I was invited to the EPIC Planning Committee meeting after October’s Epigenomes of Plants and Animals conference at the John Innes Centre, and during the meeting we discussed what I think is the biggest issue in research strategy. That inspired this post, and a probably series of posts on the EPIC website – I’ll share them when they’re up. 

Is it best to spread resources and support/fund/promote as wide a breadth of research as possible, or focus on a few areas in more depth?

The problem with the ‘catch-all’ approach to research funding is that it inevitably does not catch all. In the UK plant science is funded via the BBSRC, and a large part of that funding is allocated through a committee-determined responsive mode structure. As the committees, made up of jobbing scientists, are only gently guided by broad strategic priorities, this is essentially catch-all. However, some plant science areas now occupy very small niches and are in danger of extinction. Plant and pathogen taxonomy, physiology, soil science and some plant species, even those of economic value like ornamental flowers, soft fruits and many vegetables, have all been neglected.

The alternative is to try and deliver an effective strategy for a few areas, ensuring that these areas have a healthy, broad basic research base from which any innovations that arise can efficiently be turned into commercial product. The difficulty is, of course, deciding which areas to focus on. The decision cannot be driven by fashions or trends, nor unduly influenced by current strengths and expertise, which are all reasons for gaps in the catch-all approach. Modelling and predicting global and local challenges, other countries’ research strategies, risk of failure and impact of success, existing expertise and facilities – these and many more factors should all be considered.

It would be a cop-out to write this post and not say what my opinion is. This issue is of course far more complex than this article allows, and there has to be flexibility in any system. There are big, bad consequences of choosing the wrong areas to invest in, but there are similar, unpredictable, ramifications to accidental skills gaps in both basic and translational science caused by thinly spread funding. So my inclination is to think that within a hypothetical altruistic and infinitely flexible innovation ecosystem, the world would be better served by a focused, in-depth strategy.

What do you think? Leave a comment or get in touch on Twitter.

Staying together: green beginnings

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Published on: November 5, 2013
This seaweed, Ulva linza, would only exist as undifferentiated cells if not for bacterial signals

The second of our series of blog posts Celebrating Basic Plant Science is written by Juliet Coates, Lecturer in Molecular Genetics at the University of Birmingham.

Living organisms can be categorised in a number of ways, but one very obvious “either/or” distinction is between organisms that are made up of a single cell – unicellular organisms – and those that are many-celled, or multicellular.

The multicellular state arose many times during evolution: animals, plants, algae, amoebae, fungi and bacteria can all be multicellular. Multicellular organisms completely underpin life on Earth as we know it today – and they all must have evolved from single-celled ancestors. We understand a little of why they might have done so, as being multicellular gives a number of competitive advantages: increased size and improved nutrient collection being just two. Yet how multicellular organisms came to be is a key biological problem that is still largely unanswered.

I am a plant scientist, so I am particularly interested in the origins of multicellular green things: plants and algae. Without becoming multicellular, plants would never have colonised the land, and the evolution of multicellular plants and algae was key in shaping our climate, our ecosystems and our oxygen-rich atmosphere. How green multicellularity arose seems to me to be a really fundamental thing to understand, but it is a little-addressed question. Here I’ll give an overview of the important findings to date about the evolution of multicellularity.

 

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