Weeding the Gems

Here’s your UK Arabidopsis Research Round-up for this week.  Today we feature a mixed bag of new work from the Universities of Cambridge, Leicester, Leeds andLiverpool. One of the Leeds authors, Emily Hawkes, has been selected to present her work at GARNet 2014, which takes place in just two weeks’ time (9–10 September 2014)! If you haven’t already registered for this conference – the largest Arabidopsis conference in Europe this year, we might add! – it’s not too late to do so. Simply browse our website for more information at www.garnet2014.org and click the ‘Registration’ tab to sign up and join us in Bristol!

• Rennie EA, Ebert B, Miles GP, et al. Identification of a sphingolipid a-glucuronosyltransferase that is essential for pollen function in Arabidopsis. The Plant Cell, 1 August 2014. DOI: 10.1105/tpc.114.129171. [Open Access]

Scientists from the Universities of Cambridge and Leicester worked with American colleagues on this Plant Cell paper. It has been known for some times that glycosyl inositol phosphorylceramide (GIPC) sphingolipids make up a large proportion of the lipids in the plant plasma membrane, and that they are often decorated with glycan residues. However, until now, no glycosylating proteins have been discovered that are responsible for these residues. This group shows that the Arabidopsis thalianaprotein INOSITOL PHOSPHRYLCERAMIDE GLUCURONOSYLTRANSFERASE1 (IPUT1) transfers glucuronic acid A (GlcA) from UDP-GlcA to GIPCs. Furthermore, mutations in IPUT1 are not transmitted through pollen, suggesting that sphingolipids are essential in plants.

• Watson M, Hawkes E and Meyer P. Transmission of epi-alleles with MET1-dependent dense methylation in Arabidopsis thaliana. PLOS ONE, 19 August 2014. DOI: 10.1371/journal.pone.0105338. [Open Access]

This is a neat paper by three researchers at the University of Leeds, in which they describe an unusual pattern of ‘dense methylation’ under the control of METHYLTRANSFERASE1 (MET1). This protein is found to be responsible for three different methylation contexts: CG, CHG and CHH (where H represents A, C or T). Epi-alleles of dense methylation at non-coding RNA loci are stably maintains and transmitted in genetic crosses, suggesting that at certain loci MET1 is able to create transcriptional diversity based on the generation of independent epi-alleles. Though rare in Arabidopsis, it will be interesting to explore the possibility that MET1 is a contributor to epigenetic diversity in other plant species.

Emily Hawkes, middle author on this paper, was selected to give an oral presentation of her abstract at GARNet 2014. So, if you haven’t already registered, do so today and join us in Bristol to hear more about her work!

• Parry G. Components of the Arabidopsis nuclear pore complex play multiple diverse roles in control of plant growth. Journal of Experimental Botany, 27 August 2014. DOI: 10.1093/jxb/eru346. [Open Access]

Geraint Parry from the University of Liverpool here presents evidence to suggest that nucleoporins – involved in nuclear pore complexes (NPCs) that facilitate movement of RNA and protein between the nucleus and cytoplasm – may play distinct roles in nuclear transport. In Arabidopsis lines with defective nucleoporins in NPCs, it was noted that nuclear export of mRNA is differentially affected.

These Arabidopsis Research Round-ups are usually posted on the main GARNet website (and still will be) but we’re also going to start posting them here. We were recently approached by the Arabidopsis Information Portal to ask if we could make the Round-ups available for their website too, and it’s easier for us to do that from the blog. Long story…but enjoy!

This week we have 10 new papers published from the end of July to the middle of August, including one by our very own Charis Cook!

• De Jong M, George G, Ongaro V, Williamson L, Willetts B, Ljung K, McCulloch H and Leyser O. Auxin and strigolactone signaling are required for modulation of Arabidopsis shoot branching by N supply. Plant Physiology, 21 July 2014. DOI: 10.1104/pp.114.242388. [Open Access]

Led by GARNet’s founder Ottoline Leyser from the University of Cambridge, this paper also involved UK plant science researchers from The Sainsbury Laboratory, Cambridge, the University of York and the Swedish University of Agricultural Sciences. Here the finding is presented that nitrate limitation results in increased auxin export from active buds, leading to reduced shoot branching and a characteristic shift in relative biomass allocation to the root.

• Rautengarten C, Ebert B, Moreno I et al. The golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis.Proceedings of the National Academy of Sciences of the USA, 22 July 2014. DOI: 10.1073/pnas.1406073111. [Open Access]

Paul Dupree and Jennifer Mortimer from the University of Cambridge are listed as authors on this PNAS paper. In order to understand more about nucleotide sugar transporting (NST) proteins and their substrate-specific actions, this team have developed a novel approach to reconstitute NSTs into liposomes and subsequently analyse nucleotide sugar uptake  by mass spectrometry. Using this approach, and by synthesizing UDP-L-rhamnose in a newly developed two-step reaction, it has been possible to identify and characterize six bifunctional UDL-L-Rha/UDP-D-galactose transporters. This work is supported by evidence from loss-of-function and overexpression Arabidopsis lines.

• Yang H, Howard M and Dean C. Antagonistic roles for H3K36me3 and H3K27me3 in the cold-induced epigenetic switch at Arabidopsis FLC. Current Biology, 24 July 2014. DOI: 10.1016/j.cub.2014.06.047. [Open Access]

Led by Professor Caroline Dean at the John Innes Centre, this paper in Current Biology unpicks the epigenetic mechanism behind the switching on and off of the FLCgene, which is responsible for the onset of vernalisation after a period of cold. It is found that the histone modification H3K36me3 causes the FLC gene to be active, while an alternate modification, H3K27me3, switches the gene off again. It is thought that accumulation of these opposing histone modifications allow the plant to register how long it has been exposed to cold, so that it knows when to start flowering.

You can read more about this research on our Latest News page here: How Plants Remember Winter, and Other Stories.

• Smith S, Osman K and Franklin FCH. The condensin complexes play distinct roles to ensure normal chromosome morphogenesis during meiotic division in Arabidopsis. The Plant Journal, 26 July 2014. DOI: 10.1111/tpj.12628.

In a collaboration between the University of Birmingham and Durham University, this paper in The Plant Journal presents new information about meiosis in Arabidopsis. Specifically, the group looked at condensins – proteins involved in the organization of chromosomes during meiosis – and found distinct roles for condensin I and condensin II.

• Bardou F, Ariel F, Simpson CG, Romero-Barrios N, Laporte P, Balzergue S, Brown JWS and Crespi M. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Developmental Cell, 28 July 2014. DOI: 10.1016/j.devcel.2014.06.017.

In this article, Craig Simpson and John Brown from the James Hutton Institute in Scotland worked with French colleagues to present the finding that nuclear speckle RNA-binding protein (NSR) and the alternative splicing competitor long noncoding RNA (ASCO-lncRNA) work together as a regulatory module to control alternative splicing patterns of transcription in Arabidopsis.  Furthermore, it is found that auxin induces a major change in the alternative splicing patterns of many genes, a response largely dependent on NSRs.

• Rasool B, Karpinska B, Konert G, Durian G, Denessiouk K, Kangasjärvi S and Foyer CH. Effects of light and the regulatory Beta subunit composition of protein phosphatase 2A on the susceptibility of Arabidopsis thaliana to aphid (Myzus persicae) infestation. Frontiers in Plant Science, 29 July 2014. DOI: 10.3389/fpls.2014.00405. [Open Access]

The Foyer Lab at the University of Leeds takes the helm on this new research paper investigating the effects of light and the composition of the regulatory B-subunit of protein phosphatase 2A on aphid fecundity and plant susceptibility to Pseudomonas syringae infection. Low light-grown Arabidopsis thaliana mutant lines were used, defective in phosphatase regulatory subunit B’γ (gamma; pp2a-b’γ), B’ζ (zeta; pp2a-b’ζ1-1 and pp2a-b’ζ 1-2) or gamma zeta double mutants (pp2a-b’γζ), in the presence or absence of a high light pre-treatment. Findings suggest that pre-exposure of plants to high light, and the composition of B-subunits are important in regulating plant resistance to aphids.

• Becker JD, Takeda S, Borges F, Dolan L and Feijó JA. Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature. BMC Plant Biology, 1 August 2014. DOI: 10.1186/s12870-014-0197-3. [Open Access]

Researchers working on this paper, including those from the John Innes Centre and the University of Oxford, developed a new method for isolating growing and mature root hair cells to better analyse their transcriptomes my microarray analysis. By comparing the transcriptomes of these root hair cells with those of pollen tubes, the team found a statistical relationship between the datasets, suggesting a common transcriptional profile pattern for the apical growing cells in a plant. This study will underpin the further genetic and physiological dissection of the mechanisms underlying apical growth of plant cells.

• Cook C, Francocci F, Cervone F, Bellincampi D, Bolwell PG, Ferrari S and Devoto A. Combination of pretreatment with white rot fungi and modification of primary and secondary cell walls improves saccharification. BioEnergy Research, 5 August 2014. DOI: 10.1007/s12155-014-9512-y. [Open Access]

Here’s a paper from GARNet’s very own communication and liaison officer, Charis Cook! The final paper to be published from her PhD in the Devoto lab at Royal Holloway, here Charis et al describe how pre-treating biomass with two types of white rot fungi can improve saccharification and thus increase the accessibility of cellulose in the cell wall. The work was done in tobacco and in Arabidopsis thaliana lines with reduced de-esterified homogalacturonan content.

• Mitchell K, Brown I, Knox P and Mansfield J. The role of cell wall-based defences in the early restriction of non-pathogenic hrp mutant bacteria in Arabidopsis. Phytochemistry, 6 August 2014. DOI: 10.1016/j.phytochem.2014.07.015.

Scientists from the Universities of Kent, Leeds and Imperial College London studied the effects of challenging Arabidopsis leaves with an hrp mutant strain ofPseudomonas syringae. It was found that, although they remained viable, hrp mutant bacteria were restricted in growth within 6 hours, and the plant accumulated for H₂O₂ and peroxidase around the mutant than in the wild type. The results suggest that the generation of H₂O₂ could be a likely target for effector proteins injected into plant cells by the wild-type bacteria.

• Koster T, Meyer K, Weinholdt C, Smith LM, Lummer M, Speth C, Grosse I, Weigel D and Staiger D. Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis. Nucleic Acids Research, 7 August 2014. DOI: 10.1093/nar/gku716.

Lisa Smith from the University of Sheffield worked with German colleagues on this Nucleic Acids Research paper. It is already known that the hnRNP-like glycine-rich RNA-binding protein AtGRP7 regulates pre-mRNA splicing in Arabidopsis, but here it is shown the AtGRP7 as has an effect on miRNA levels in the plant. Arabidopsis lines overexpressing AtGRP7 showed a significant reduction in the level of 30 different miRNAs, and an increase in a further 14; RNA immunoprecipitation also revealed that AtGRP7 interacts directly wit the pri-miRNAs in vivo.