26th Jan 2017

The papers that feature in this weeks Research Roundup touch on different aspects of research conducted in Arabidopsis. Firstly Alastair McCormick (University of Edinburgh) uses Arabidopsis as a tool to study the factors that control the activity of Rubisco. Secondly Vinod Kumar (John Innes Centre) uses the power of Arabidopsis genetics to assess the relationship between components involved in light signaling. Thirdly Jerry Paszkowski (SLCU) takes advantage of the enormously detailed Arabidopsis genome information to search for patterns that control the formation of transgenerational epialleles. The next paper is from Peter Eastmond and Smita Kurup at Rothamsted and investigates the alteration in cellular fatty acid composition following temperature changes. Finally Sarah McKim (University of Oxford) is a co-author on a paper that looks at the differences between the signaling modules that control floral development in Arabidopsis and Cardamine.

Atkinson N, Leitão N, Orr DJ, Meyer MT, Carmo-Silva E, Griffiths H, Smith AM, McCormick AJ (2017) Rubisco small subunits from the unicellular green alga Chlamydomonas complement Rubisco-deficient mutants of Arabidopsis. New Phytol. http:/​/​dx.​doi.​org/10.1111/nph.14414

Open Access

Alistair McCormick (University of Edinburgh) provides an audio description of this paper in which he collaborates with UK colleagues in Norwich, Cambridge and Lancaster. This study aims to improve photosynthetic efficiency by introducing a component of the algal carbon concentrating mechanisms (CCMs) into the chloroplasts of higher plants. One mechanism for improving efficiency is brought about by the binding of rubisco (RBS) in a pyrenoid structure. In this study they replace an Arabidopsis RBS small subunit (SSU) with that from the algae Chlamydomonas reinhardtii and showed that a hybrid RBS complex formed with similar catalytic properties as that of the wildtpye complex. However the photosynthetic rate in these RBS complexes was reduced, demonstrating that the RBS SSU is key for determining the catalytic properties of the whole enzyme.

Alistair discusses this paper on the GARNet YouTube channel.

Gangappa SN, Kumar SV (2016) DET1 and HY5 Control PIF4-Mediated Thermosensory Elongation Growth through Distinct Mechanisms. Cell Rep. http:/​/​dx.​doi.​org/10.1016/j.celrep.2016.12.046

Open Access

Vinod Kumar (John Innes Centre) features in the ARR for the second consectutive week with a manuscript that again focuses on the transcription factor PIF4 and its role as a central signaling hub that integrates environmental cues to control growth. Here his lab looks at the signaling factors that feed into the PIF4 module and demonstrate that DET1/COP1 and HY5 control thermosensory growth via distinct mechanisms, the former by stabilising the PIF4 protein and the latter by competitively binding to PIF4 targets and not directly affecting the protein itself.

Vinod discusses this paper on the GARNet YouTube channel.

Over the past few weeks work from Phil Wigge, Kerry Franklin or Vinod Kumar has moved on our understanding of how PIF4 integrates environmental signals, demonstrating the strength of UK science in this key area of fundamental plant developmental biology. This work is summarised in a post on the GARNet blog

Catoni M,, Griffiths J, Becker C, Zabet NR, Bayon C, Dapp M, Lieberman-Lazarovich M, Weigel D, Paszkowski J (2017) DNA sequence properties that predict susceptibility to epiallelic switching EMBO J.


Open Access

Jerry Paszkowski (SLCU) is the lead author on this paper that collaborates with the lab of Detlef Weigel (Max Planck Tubingen). In this study they investigate the phenomonen of transgenerationally epigenetic inheritance through alleles established by the activity of MET1. They assessed genome-wide methylation in partial and null met1 plants, which allowed them to identify cytosine residues as candidate epialleles compared to those that are unlikely to be inherited. This allowed the establishment of general features that characterise genomic regions that include epialleles. These features were confirmed throughout Arabidopsis ecotypes, in epigenetic recombinant inbred lines (epiRILs) and also in rice, confirming that the factors important for determining the location of epialleles might determined by sequence features and not by the host organism.

Menard G, Martin Moreno J, Bryant F, Munoz-Azcarate O, Kelly AA, Hassani-Pak K, Kurup S, Eastmond PJ (2017) Genome wide analysis of fatty acid desaturation and its response to temperature. Plant Physiol.

http:/​/​dx.​doi.​org/10.1104/pp.16.01907 Open Access

Peter Eastmond and Smita Kurup (Rothamstead Research) lead this study that sheds light on the role that cellular fatty acid (FA) mobilisation plays in the respond to temperature. In response to this environmental cue plants alter their membrane and storage FA composition by modulating the activity of the microsomal ω-6 and ω-3 fatty acid desaturases, FAD2 and FAD3. This study shows that increased temperature prevents ω-6 and ω-3 FA desaturation and that there is significant natural variation in this process. The authors conducted QTL and GWAS studies using the multi-parent advanced generation inter-cross (MAGIC) population to define a cis-acting 5’ untranslated region of FAD2 as important in control of this process. Interestingly they also identified a separate QTL on a different chromosome that controls the temperature responsiveness of ω-6 FA alterations. They are currently searching for the precise genetic identify of this QTL.

Monniaux M, McKim SM, Cartolano M, Thévenon E, Parcy F, Tsiantis M, Hay A (2017) Conservation vs divergence in LEAFY and APETALA1 functions between Arabidopsis thaliana and Cardamine hirsuta.

New Phytol. http:/​/​dx.​doi.​org/10.1111/nph.14419

Sarah McKim (University of Oxford) is a co-author on a study led by Angela Hay at the Max-Planck Koln who used to also work in Oxford. They look at floral patterning in Arabidopsis and in the closely related species Cardamine hirsuta. They identified versions of leafy (LFY) and apetala (AP1) responsible for patterning in C.hirsuta. Unlike in Arabidopsis, AP1 activation is fully dependent on LFY showing that even though the same genes are involved in this process their regulatory network appears to differ between the two species.