Arabidopsis Research Roundup: April 14th

This week Arabidopsis Research Roundup contains two studies that originate at the University of Birmingham. Firstly George Bassel kindly provides an audio description of a study that looks at the processes regulating seed germination. Secondly Juliet Coates leads an investigation into the function of evolutionarily conserved ARABIDILLO proteins. Elsewhere is a University of Edinburgh study into the tissue-specificity of PhyA responses and lastly an investigation of the phytotoxic effects of Cerium nanoparticles.

Nieuwland J, Stamm P, Wen B, Randall RS, Murray JA, Bassel GW (2016) Re-induction of the cell cycle in the Arabidopsis post-embryonic root meristem is ABA-insensitive, GA-dependent and repressed by KRP6. Sci Rep. http://dx.doi.org/10.1038/srep23586 Open AccessRootTip

George Bassel (Birmingham), GARNet PI Jim Murray (Cardiff) and Jeroen Nieuwland (South Wales) are the leaders of this study that investigates the activation of the root meristem during germination, a process that requires de novo GA synthesis. Using hormone applications and genetic analysis the authors show that root meristem can begin elongation independent of germination, which is defined as occurring following both testa rupture and radicle protrusion. KRP6 is a cell cycle regulator and partially represses activation of the cell cycle by GA so krp6 mutants germinate more rapidly. Overall this study concludes that the cell cycle can uncouple the interactions of GA and ABA that act to conclude germination and promote root meristem elongation.

George Bassel kindly provides a short audio description of this paper.

Moody LA, Saidi Y, Gibbs DJ, Choudhary A, Holloway D, Vesty EF, Bansal KK, Bradshaw SJ, Coates JC (2016) An ancient and conserved function for Armadillo-related proteins in the control of spore and seed germination by abscisic acid. New Phytol. http://dx.doi.org/10.1111/nph.13938 Open Access

This study comes exclusively from the University of Birmingham and is led by Juliet Coates. This group investigates the role of Armadillo-related ARABIDILLO proteins on branching processes across plant species. In the moss Physcomitrella patens these proteins are linked to the action of the hormone ABA on spore germination, which converges with a role for the proteins in Arabidopsis seed germination. Importantly both P.patens and Selaginella moellendorffii ARABIDILLO proteins are able to substitute for native proteins in Arabidopsis, demonstrating their conserved function. The authors conclude that these proteins were co-opted into the regulation of both sporophytic and gametophytic processes early in plant evolution.

Kirchenbauer D, Viczián A, Ádám É, Hegedűs Z, Klose C, Leppert M, Hiltbrunner A, Kircher S, Schäfer E, Nagy F (2016) Characterization of photomorphogenic responses and signaling cascades controlled by phytochrome-A expressed in different tissues. New Phytologist . http://dx.doi.org/10.1111/nph.13941 Open Access

Ferenc Nagy (Edinburgh) is the corresponding author of this Hungaro-German study that focuses on how phytochrome responses are mediated in a tissue-specific manner. Considering that phyA is expressed throughout plant tissues it remained a mystery as to how the PhyA responses are able to control plant development. This study used tissue-specific promotors to drive PHYA production in a variety of tissues and discovered that expression in a limited number of tissues is able to regulate flowering time and root growth. In addition they find evidence for the intercellular movement of PhyA. The authors conclude that the PhyA response is partly controlled by a mix of tissue-specific expression and the regulation of key downstream factors in a tissue-autonomous cell activity.

Yang X, Pan H, Wang P, Zhao FJ (2016) Particle-specific toxicity and bioavailability of cerium oxide (CeO2) nanoparticles to Arabidopsis thaliana J Hazard Mater. http://dx.doi.org/10.1016/j.jhazmat.2016.03.054

GraphThis Sino-UK-Australian study is led by Fang-Jie Zhao at Rothamstead Research. They investigate the uptake and phytotoxicity of commonly used (in consumer products) cerium oxide nanoparticles (CeO2-NPs) into Arabidopsis. At high concentrations the NP component, but not the Ce ions, were shown to have toxic effects on plant growth. These CeO2-NPs were taken up and translocated to the shoot where they aggregate in needle-like particles. This movement was independent of the type or concentation of Ce. The authors suggest this represents important information for the environmental considerations linked to the use and disposal of this type of NPs.

Brassica Research Report: 2015

The Arabidopsis Research Roundup has been put to bed for 2015 so in the leadup to the Christmas we’ll take a look at some of the papers that have been published in 2015 by UK researchers working ondifferent plants.
Today we focus on Brassica species and by looking at papers from throughout 2015 this selection touches on a broad selection of research areas. Chronologically first is a study from Nottingham University that looks at the ability of Brassica rapa to take up specific elements, such as Zn, Ca and Mg. Secondly is a study that documents the parameters that make different cultivars of Brassica napus useful in biorefining. Thirdly we highlight where Brassica oleracea has been used both in preference to, and alongside Arabidopsis in a study that investigates meiotic recombination. Next is a study that investigates the relationship between leaf colour and insect herbivory. Finally we highlight a recent publication from the John Innes Centre that demonstrates the ability to generate gene-edited B.oleracea.
The varieties of Brassica
March

Blasco B, Graham NS, Broadley MR (2015) Antioxidant response and carboxylate metabolism in Brassica rapa exposed to different external Zn, Ca, and Mg supply.
J Plant Physiol. 176:16-24 http://dx.doi.org/10.1016/j.jplph.2014.07.029
Martin Broadley and Neil Graham from Nottingham University lead this study that investigates antioxidant response and carboxylate metabolism in Brassica rapa. The authors looked at these parameters in the presence of varying amounts of zinc, calcium or magnesium in experiments that aimed to simulate the response to deficiency or toxicity of these elements. Plants grown with high concentrations of these elements showed increased shoot biomass, hydrogen peroxide, total ascorbate and increasing activity of enzymes involved in removal of antioxidants. This indicates that B.rapa is particularly sensitive to high levels of these elements. The information provided in this study represents important baseline measurements that will aid the future characterisation of B.rapa TILLING lines, generated by the RevGenUK service at the JIC.

July

Wood IP, Wellner N, Elliston A, Wilson DR, Bancroft I, Waldron KW (2015) Effect of Brassica napus cultivar on cellulosic ethanol yield. Biotechnol Biofuels. 8:99. http://dx.doi.org/10.1186/s13068-015-0278-z Open Access
Keith Waldron (Institute of Food Research, JIC) leads this collaboration with the University of York that investigates how the sugar composition of Brassica napus alters its ability to be used as a source for biorefining. They found significant differences in the saccharification and fermentation yields after the processing of straw obtained from 17 different B.napus cultivars. Surprisingly glucan-rich straw was not correlated with higher saccharification or ethanol yields but rather the non-cellulosic components were more reliable indicators of substrate quality, with the amount of pectins and arabinogalactans having the greatest impact on saccharification. Ultimately this study finds that pectin concentration is most likely to determine to effectiveness of the cultivar in the production of bioethanol. This is important information for the future development of different dicot species for use in this aspect of biorefining.

July

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 http://dx.doi.org/10.1371/journal.pgen.1005372 Open Access

Immunolocalisation of proteins during meiotic recombination in Brassica.
Immunolocalisation of proteins during meiotic recombination in Brassica.

Chris Franklin (Birmingham) is the leader on the UK-US-Austrian collaboration that looks at the role of the PCH2 protein during meiotic recombination. Although much of this study uses Arabidopsis mutant plants, the initial immunoprecipitations that led to identification of novel factors were performed using pollen mother cells from Brassica oleracea. Subsequently some important imaging also takes place in B.oleracea. The authors use structured illumination microscopy (SIM) to investigation the localisation of synaptonemal complex formation during meiosis and the close relationship between Arabidopsis and B.oleracea allowed the authors to use to same reagents fo these experiments. This paper was featured in an Arabidopis Research Roundup earlier in the year.

September.

Green JP, Foster R, Wilkins L, Osorio D, Hartley SE (2015) Leaf Colour as a Signal of Chemical Defence to Insect Herbivores in Wild Cabbage (Brassica oleracea). PLoS One 10(9):e0136884 http://dx.doi.org/10.1371/journal.pone.0136884 Open Access

This collaboration between York and Sussex Universitites is led by Sue Hartley and Daniel Osorio and look into the role that leaf colour plays in the defence response in wild cabbage. This aspect of plant physiology has been proposed as being important in defence against insect herbivory but this is the first instance where real data from wild populations has been obtained on this topic. The authors found that variation in leaf colour and brightness corresponded to particular glucosinolate levels as well as of the ability of certain herbivores to colonise the leaves. As might be predicted, leaves with lower levels of glucosinolate coincided with faster growth rates of lepidopteran larvae. However in a controlled experiment neither adult butterflies or adult aphids showed a preference for leaves of different colours. This therefore might suggest that although in the field herbivores may benefit from colonising leaves with lower defence chemicals (and an altered colour), the adults do not have the ability to select for these particular leaves, indicating that selection of leaves is either down to chance or other uninvestigated parameters.

November.

Lawrenson T, Shorinola O, Stacey N, Li C, Østergaard L, Patron N, Uauy C, Harwood W (2015) Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease Genome Biol. 16:258. http://dx.doi.org/10.1186/s13059-015-0826-7 Open Access

An example of successfully gene edited Brassica. From Genome Biology
An example of successfully gene edited Brassica. From Genome Biology

This is a collaboration between Wendy Harwood, Cristobal Uauy, Nicola Patron and Lars Ostargaard from the John Innes Centre and the Sainsbury Lab in Norwich. Over the past few years, CRISPR-Cas technology has been presented as important technology to be used in the future generation of gene edited crops. However only a few studies have been published to date where this technology has been effectively used. This paper describes the use of CRISPR-Cas to generate specific mutations in both barley and Brassica oleracea. Across both species they identified targeted mutations in 10%-25% of the first generation plants although interestingly they were also able to identify B.oleracea mutants in the T0 generation. They also observed off-target activity in both species even though the designed guide RNAs contains mismatches with the incorrectly edited sequences.
This is important work demonstrating that this type of gene editing can be used to rapidly generate stable mutants in crop species. The creation of mutants in off-target genes is a potential concern from a regulatory perspective although can be viewed as a positive factor for targeting multigene families that do not have appropriate identical target sequences.

Arabidopsis Research Roundup: November 13th.

This weeks Arabidopsis Research Roundup presents a wide range of topics from researchers across the UK. Firstly we highlight a study that documents the early stages of a potential biotechnological/synthetic biology approach to improve higher plant photosynthesis using algal components. Corresponding author Alistair McCormick also takes five minutes to discuss this work. Secondly a team based mostly at Bath introduces the function of the PAT14 gene, which is involved in S-palmitoylation. Thirdly is a study that successfully transfers SI components between evolutionary diverged plant species and the final paper documents research that adds additional complexity to the signalling pathway that responses to strigolactones.

Atkinson N, Feike D, Mackinder LC, Meyer MT, Griffiths H, Jonikas MC, Smith AM, McCormick AJ (2015) Introducing an algal carbon-concentrating mechanism into higher plants: location and incorporation of key components. Plant Biotechnol J. http://dx.doi.org/10.1111/pbi.12497 Open Access

This work results from a collaborative effort between the four groups that make up the Combining Algal and Plant Photosynthesis (CAPP) consortium and include Howard Griffiths (Cambridge), Martin Jonikas (Carnegie Institute for Science), Alison Smith (JIC) and Alistair McCormick (Edinburgh). Here they attempt to express in higher plants a range of algal proteins that are involved in carbon-concentrating mechanisms (CCM). They initially confirmed the intracellular locations of ten algal CCM components and showed that these locations were largely conserved when the proteins were expressed transiently in tobacco or stably in Arabidopsis. Although the expression of these CCMs components in Arabidopsis didn’t enhance growth, the authors suggest that stacking of multiple CCM proteins might be needed to confer an increase in productivity.

Alistair takes five minutes to discuss this paper here:

Li Y, Scott RJ, Doughty J, Grant M, Qi B (2015) Protein S-acyltransferase 14: a specific role for palmitoylation in leaf senescence in Arabidopsis. Plant Physiology http://dx.doi.org/10.1104/pp.15.00448 Open Access

This Southwest-based study is led by Baoxiu Qi from the Plant-Lab at Bath University with input from Murray Grant (Exeter). They investigate Protein S-Acyl Transferase (PATs) protein, which are multi-pass transmembrane proteins that catalyze S-acylation (commonly known as S-palmitoylation). This process both confers correct protein localisation and is involved in signalling. These are 24 PATs in Arabidopsis and this study focuses on the novel PAT14, which they show has its predicted enzymatic role. Pat14 mutant plants show accelerated senescence that is associated with SA, but not JA or ABA-signaling. Therefore the authors suggest that AtPAT14 plays a pivotal role in regulating senescence via SA pathways and that this is the first published linkage between palmitoylation and leaf senescence.

Lin Z1, Eaves DJ1, Sanchez-Moran E1, Franklin FC1, Franklin-Tong VE1 (2015) The Papaver rhoeas S determinants confer self-incompatibility to Arabidopsis thaliana in planta Science 350(6261):684-7 http:/​/​dx.​doi.​org/​10.1126/science.aad2983

University of Birmingham researchers led by Noni Franklin- Tong publish this study in Science in which they transfer the elements that confer self-incompatibility (SI) in Papever rhoeas (Poppy) to Arabidopsis. They find that Arabidopsis pistils that express the self-determinant PrsS protein reject pollen that expresses the PrpS protein. This leads to a robust SI response in these plants, demonstrating that these two components are sufficient for the establishment of this interaction. Poppy and Arabidopsis are evolutionarily separated by 140million years so the authors suggest that the successful transfer of SI determinants between these divergent species will have potential utility in future crop production strategies.

Soundappan I, Bennett T, Morffy N, Liang Y, Stanga JP, Abbas A, Leyser O, Nelson DC (2015) SMAX1-LIKE/D53 Family Members Enable Distinct MAX2-Dependent Responses to Strigolactones and Karrikins in Arabidopsis The Plant Cell http://dx.doi.org/10.1105/tpc.15.00562

Ottoline Leyser (SLCU) is the UK lead on this US-UK collaboration that investigates the plant response to butenolide signals, namely the plant hormone strigolactones and smoke-derived karrikins. It is known that these molecules are perceived by the F-box protein MORE AXILLARY GROWTH2 (MAX2) and that the Arabidopsis SUPPRESSOR OF MAX2 1 (SMAX1) protein acts downstream of this perception. This study documents an extensive genetic study that shows that the activity of the SMAX1-LIKE genes, SMXL6, SMXL7, and SMXL8 promote shoot branching. smxl6,7,8 mutant plants suppress several strigolactone-related phenotypes in max2, that focus on the response to auxin but not on germination or hypocotyl elongation responses, which are only suppressed in smax1 mutants. On a molecular level these responses are controlled by the MAX2-dependant degradation of the SMAX1/SMXL proteins, which result in changes in gene expression. Therefore this shows that the diversity of SMAX1/SMXL proteins allows the signaling pathway that responses to butenolide signals to bifurcate downstream of the initial perception.

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