17th Apr 2014

Apologies that there has been no Arabidopsis Research Round-up for a couple of weeks; it has been a busy time for the GARNet team! Firstly we visited the University of Reading for the Monogram Annual Meeting, then we were off to York for PlantSci 2014, where we launched our report on Synthetic Biology (PDF).

Last week we held a Software Carpentry workshop at the University of Warwick – you can see some photos from the workshop on our blog:

So, as there has been no Round-up for a while, we have a bumper edition for you today with 14 new Arabidopsis papers from around the UK – that should give you plenty to read over the Easter break!


  • Doughty J, Al-Jabri M and Scott RJ. Flavonoids and the regulation of seed size in Arabidopsis. Biochemical Society Transactions, 10 February 2014. DOI: 10.1042/BST20140040.

Unfortunately I hit an impenetrable paywall with this paper (Open Access Button clicked!) but James Doughty, PhD student Maha Al-Jabri and Rod Scott from the University of Bath present a review of the major regulators of seed size in Arabidopsis, focusing largely on the role of flavonoids produced in the endothelium of the seed coat.


  • Sambade A, Findlay K, Schäffner AR, Lloyd CW and Buschmann H. Actin-dependent and independent functions of cortical microtubules in the differentiation of Arabidopsis leaf trichomes. The Plant Cell, 20 February 2014. DOI: ​10.1105/tpc.113.118273.

Cell and developmental biologists from the John Innes Centre worked with German colleagues on this Plant Cell paper, in which they use the tortifolia2 mutant of Arabidopsis thaliana to study the role of microtubules in plant cell differentiation. tortifolia2 has a microtubule defect caused by a point mutation, which in turn causes overbranching and right-handed helical growth in the single-cells leaf trichomes. Results suggest there is a genetic interaction between actin and microtubules. 


  • Kellermeier F, Armengaud P, Seditas TJ, Danku J, Salt DE and Amtmann A. Analysis of the root system architecture of Arabidopsis provides a quantitative readout of crosstalk between nutritional signals. The Plant Cell, 12 March 2014. DOI: 10.1105/tpc.113.122101.

Led by Anna Amtmann from the University of Glasgow, and also involving GARNet committee member David Salt from the University of Aberdeen, this paper presents new knowledge of the effects of nitrogen, potassium, phosphorus, sulphur and light on the nature of root system architecture and how plants integrate multiple nutritional stimuli into complex developmental programs.


  • Lee EK, Regan Lucas J, Goodrich J and Sack FD. Arabidopsis guard cell integrity involves the epigenetic stabilization of the FLP and FAMA transcription factor genes. The Plant Journal, 22 March 2014. DOI: 10.1111/tpj.12516.

Justin Goodrich from the University of Edinburgh collaborated with a Canadian team to contribute to this paper on Arabidopsis guard cell fate. They looked at the epigenetic factors contributing to stomatal development and stability.


  • Tryfona T, Theys TE, Wagner T, Stott K, Keegstra K and Dupree P. Characterisation of FUT4 and FUT6 a-(1à2)-fucosyltransferases reveals that absence of root arabinogalactan fucosylation increases Arabidopsis root growth salt sensitivity. PLOS ONE, 25 March 2014. DOI: ​10.1371/journal.pone.0093291.

Members of the Dupree lab at the University of Cambridge, along with US collaborators, have been studying the control of fucosylation in arabinogalactan polysaccharides (AGPs) in Arabidopsis thaliana, and the functions of those fucosylations. It was found that FUT4 is solely responsible for AGP fucosylation in leaves, but that FUT6 also fucosylates the same sites, suggesting at least partial redundancy. Fucosylation of AGPs is thought to be important in maintaining proper cell expansion under salt stress.


  • Masakapalli SK, Bryant FM, Kruger NJ and Ratcliffe RG. The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a flexible balance between the cytosolic and plastidic contributions to carbohydrate oxidation in response to phosphate limitation. The Plant Journal, 27 March 2014. DOI: ​10.1111/tpj.12522.

In this Plant Journal paper, scientists from the University of Oxford propose that plant cells respond to phosphate deprivation by reconfiguring the flux distribution through the pathways of carbohydrate oxidation to take advantage of better phosphate homeostasis in the plastid.  


  • Krüssel L, Junemann J, Wirtz M, et al. The mitochondrial sulfur dioxygenas ETHE1 is required for amino acid catabolism during carbohydrate starvation and embryo development in Arabidopsis thaliana. Plant Physiology, 31 March 2014. DOI: ​10.1104/pp.114.239764.

Luke Browning and Jeremy Thornton from the John Innes Centre worked with a German-led team of researchers to investigate the biochemical and physiological functions of ETHE1 in Arabidopsis thaliana. ETHE1 is known to catalyse the oxidation of persulphides in the mitochondrial matrix, and it is essential for early embryo development. In this study, another role for ETHE1 was identified; the oxidation of branched-chain amino acids and lysine.


  • Van Erp H, Kelly AA, Menard G and Eastmond PJ. Multi-gene engineering of triacylglycerol metabolism boosts seed oil content in Arabidopsis. Plant Physiology, 1 April 2014. DOI: ​10.1104/pp.114.236430.

Led by Peter Eastmond, scientists from Rothamsted Research are trying to increase the oil yield of oilseed crops through genetic engineering. Three genes had previously been identified as contributors to the enhancement of seed oil content, but it was unknown whether there was an additive effects of all three of these genes. Using Arabidopsis as a model, the researchers discovered that, in plants expressing WRINKLED1 and DIACYLGLYCEROL ACYLTRANSFERASE1, together with suppression of SUGAR-DEPENDENT1, while seed number decreased, oil yield was indeed greater.  


  • MacLean AM, Orlovskis Z, Kowitwanich K, Zdziarska AM, Angenent GC, Immink RGH and Hogenhout S. Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner. PLOS Biology, 8 April 2014. DOI: ​10.1371/journal.pbio.1001835.

This high-profile paper from the lab of Saskia Hogenhout at the John Innes Centre (with Dutch colleagues) discusses the finding that Phytoplasma pathogens alter the host plant’s ability to produce flowers, instead converting them into vegetative tissue which helps to support the pathogen’s lifecycle. You can read more about this paper in the article on our website here: How Phytoplasma turn their plant hosts into their living-dead servants.


  • Basak I, Pal R, Patil KS, et al. Arabidopsis AtPARK14m, which confers thermotolerance, targets misfolded proteins. Journal of Biological Chemistry, 9 April 2014. DOI: ​10.1074/jbc.M114.548156.

This paper, whose author list includes Diluka Peiris and Mark Odell from the University of Westminster, makes an interesting link between proteins implicated in human Parkinson’s Disease and homologues in Arabidopsis thaliana. Human PARK13 (hPARK13) is a neuroprotective serine protease, although how it confers stress protection is as yet unknown. Meanwhile, AtPARK13 is also a mitochondrial protease; its expression is induced by heat stress and it confers thermotolerance by degrading misfolded protein targets. Could this provide new insights into the role of PARK13 is neurodegeneration?


  • Smolarkiewicz M, Skrzypczak T, Michalak M, Lesniewicz K, Walker JR, Ingram G and Wojtaszek P. Gamma-secretase subunits associate in intracellular membrane compartments in Arabidopsis thaliana. Journal of Experimental Botany, 10 April 2014. DOI: ​10.1093/jxb/eru147.

Another paper linking Arabidopsis homologues with proteins implicated in human disease! This time, the focus of the paper is gamma-secretase, a multisubunit complex that is linked with Alzheimer’s Disease. The UK researchers involved are plant scientists Ross Walker and Gwyneth Ingram from the University of Edinburgh. Homologues of animal gamma-secretase are not only present in Arabidopsis, but the motifs crucial for gamma-secretase activity are conserved. Data presented here is consistent with those from animal studies, and could be a starting point for analysis of gamma-secretase in plants.


  • Gutiérrez J, González-Pérez S, García-García F, Daly CT, Lorenzo Ó, Revuelta JL, McCabe P and Arellano JB. Programmed cell death activated by Rose Bangal in Arabidopsis thaliana cell suspension cultures requires functional chloroplasts. Journal of Experimental Botany, 10 April 2014. DOI: ​10.1093/jxb/eru151.

The first author on this paper is Jorge Gutiérrez, then at the University of Salamanca in Spain, but now a lecturer in Food Security at the University of Surrey. In this paper, the authors aimed to gain a better understanding of singlet oxygen-mediated defense responses in plants by subjecting an Arabidopsis thaliana cell suspension culture to photooxidative damage with Rose Bengal and hydrogen peroxide. 


  • Petrillo E, Godoy Herz MA, Fuchs A, et al. A chloroplast retrograde signal regulates nuclear alternative splicing. Science, 10 April 2014. DOI: ​10.1126/science.1250322.

The penultimate paper in this week’s bumper Round-up features researchers from the James Hutton Institute in Dundee, and was published in Science. Using photosynthetic electron transfer inhibitors with different mechanisms of action, the researchers deduce that alternative splicing of a subset of Arabidopsis genes is regulated by a reduced pool of plastoquinones that in turn initiate a chloroplast retrograde signal.


  • Costa LM, Marshall E, Tesfaye M, et al. Central cell-derived peptides regulate early embryo patterning in flowering plants. Science, 11 April 2014. DOI: ​10.1126/science.1243005.

And finally, another high impact Science paper, this time from the lab of José Gutiérrez-Marcos right here at GARNet Towers (the University of Warwick). In this work the researchers demonstrate that a small cysteine-rich peptide family is required for the formation of the zygotic basal cell lineage in the early establishment of the Arabidopsis embryo. Furthermore, the second female gamete and its sexually derived endosperm regulate early embryonic patterning in flowering plants. You can read more on this story here: Plants evolve ways to control embryo growth and development