Arabidopsis Research Roundup: August 27th

The Arabdopsis Research Roundup broadens its remit this week. As well as including three original research papers, which look at casparian strip formation, light and hormone signaling, we also highlight an important viewpoint article that aims to set standards for synthetic biology parts. In addition we include a meeting report from a plant synthetic biology summer school and interviews with plant scientists at the JIC, Caroline Dean and Anne Osbourn.

Kamiya T, Borghi M, Wang P, Danku JM, Kalmbach L, Hosmani PS, Naseer S, Fujiwara T, Geldner N, Salt DE (2015) The MYB36 transcription factor orchestrates Casparian strip formation Proc Natl Acad Sci USA http://dx.doi.org/10.1073/pnas.1507691112 Open Access

GARNet Advisory Board Chairman David Salt (Aberdeen) leads this international collaboration that looks at the (relatively) poorly understood Casparian strip (CS), a lignin-based filter that lies in root endodermal cells. Formation of the CS is initiated by Casparian strip domain proteins (CASPs) that recruit other proteins, which begin the process of lignin deposition. In this study the authors look upstream this process and identify the transcription factor MYB36 that directly regulates expression of CASPs and is essential for CS formation. Ectopic expression of MYB36 in root cortical tissues is sufficient to stimulate expression of CASP1-GFP and subsequent deposit a CS-like structure in the cell wall of cortex cells. These results have implications for the design of future experiments that aim to control how nutrients are taken up by the plant as even though myb36 mutants have a ‘root-defect’, they also have changes to their leaf ionome.

Sadanandom A, Ádám É, Orosa B, Viczián A, Klose C, Zhang C, Josse EM, Kozma-Bognár L, Nagy F (2015) SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana Proc Natl Acad Sci USA http://dx.doi.org/10.1073/pnas.1415260112 Open Access

Ari Sadanandom (Durham) and Ferenc Nagy (Edinburgh) are the leaders of this study that investigates the precise function of the PhyB photoreceptor protein. PhyB interacts with a wide range of downstream signaling partners including the PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. The small ubiquitin-like modifier (SUMO) peptide is conjugated to larger proteins to bring about a variety of signaling outcomes. In this case the authors find that SUMO is preferentially attached to the C-term of PhyB under red light conditions, a relationship that occurs in a diurnal pattern. SUMOylation of PhyB prevents interaction with PIF5 whilst the OVERLY TOLERANT TO SALT 1 (OTS1) protein likely de-SUMOlyates PhyB in vivo. Altered levels of PhyB SUMOylation cause distinct light-responsive phenotypes and as such this paper adds another level of regulation to the already complex known network that controls light signaling.

Schuster C, Gaillochet C, Lohmann JU (2015) Arabidopsis HECATE genes function in phytohormone control during gynoecium development Development. http://dx.doi.org/10.1242/dev.120444 Open Access

Christopher Schuster who is now a postdoc based at the Sainsbury lab in Cambridge is the lead author on this investigation into the role of the HECATE (HEC) family of bHLH transcription factors on fruit development in Arabidopsis. During this process HEC proteins are involved in the response to both the phytohormones auxin and cytokinin, the authors proposing that HEC1 plays an essential role in Arabidopsis gynoecium formation.

Patron N et al (2015) Standards for plant synthetic biology: a common syntax for exchange of DNA parts New Phytologist http://dx.doi.org/10.1111/nph.13532 Open Access

Carmichael RE, Boyce A, Matthewman C Patron N (2015) An introduction to synthetic biology in plant systems New Phytologist http://dx.doi.org/10.1111/nph.13433 Open Access

Although not strictly based on Arabdopsis work, there are a couple of articles in New Phytologist that have broad relevance to plant scientists who are interested in plant synthetic biology. In the first of these Nicola Patron (The Sainsbury Laboratory) leads a wide consortium that aims to set parameters for the standardisation of parts in plant synthetic biology. It is hoped that as the principles of synbio are used more widley in the plant sciences that the proposals in this paper will serve as a useful guide to standidise part production. GARNet has recently written a blog post on this topic.
SynBioWorkshopPic
The associated meeting report looks at the use of plant synthetic biology in a teaching context with a synopsis of the ERASynBio summer school hosted by John Innes Centre. In this event, young researchers from a range of backgrounds were introduced to the power and potential of plant synthetic biology through a diverse course of lectures, practical session and group projects.

 

Vicente C (2015) An interview with Caroline Dean Development http://dx.doi.org/10.1242/dev.127548 Open Access

An interview with Anne Osbourn (2015) New Phytologist <a href="http://dx.doi acheter cialis.org/10.1111/nph.13616″ onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘http://dx.doi.org/10.1111/nph.13616’, ‘http://dx.doi.org/10.1111/nph.13616 ‘]);” target=”_blank”>http://dx.doi.org/10.1111/nph.13616 Open Access

These are interviews with eminent female plant molecular biologists who both work at the John Innes Centre. Caroline Dean’s lab focuses on the epigenetic mechanisms that regulate vernalisation whilst Anne Osbourn is interested in using synthetic biology approaches to engineer metabolic pathways for the production of novel compounds.

Arabidopsis Research Roundup: August 21st.

There are a wide array of topics included in this weeks Arabidopsis Research Roundup, ranging from studies on stomatal density, thylakoid transport, metabolic flux analysis, mutant detection and root development. We feature unlinked studies from three researchers from the University of Oxford Plant Science (Paul Jarvis, Lee Sweetlove and Nick Harberd), whilst the papers from Julie Gray and Brian Forde share the broad theme that investigates different mechanisms that might be used to improve nitrogen uptake, either by modifying the expression of a single gene involved in root development or by altering stomatal density.

Hepworth C, Doheny-Adams T, Hunt L, Cameron DD, Gray JE (2015) Manipulating stomatal density enhances drought tolerance without deleterious effect on nutrient uptake New Phytol. http://dx.doi.org/10.1111/nph.13598

Julie Gray (University of Sheffield) is an expert on both stomatal biology and on the potential for manipulating stomatal density to improve crop production. In this study drought tolerance and soil water retention were measured in four Arabidopsis mutants with defects in epidermal patterning and stomatal density. Nutrient uptake was measured by mass flow of 15N. Plants with less stomata had reduced transpiration and were drought-tolerant yet interestingly showed little reduction in shoot N concentrations, especially when water availability is restricted. In contrast, plants with extra stomata could take up more N except when access to water was reduced. Therefore the authors show that by altering stomatal density they can generate plants that are drought resistance yet maintain nutrient uptake or generate plants with enhancing nutrient uptake is conditions with plentiful water.

Trösch R, Töpel M, Flores-Pérez Ú, Jarvis P (2015) Genetic and Physical Interaction Studies Reveal Functional Similarities between ALB3 and ALB4 in Arabidopsis. Plant Physiol. http://dx.doi.org/10.1104/pp.15.00376

This German, Swedish and UK collaboration is led by Paul Jarvis at the University of Oxford and broadly investigates thylakoid protein targeting. The ALB3 complex has previously been shown to target light harvesting complex proteins (LHCP) to the thylakoid. A related Arabidopsis protein, ALB4, had been proposed to interact not the LHCPs but rather with the ATP synthase complex. However this study shows that ALB3 and ALB4 have some overlapping roles in addition to their specific functions and that they can engage with a similar set of interactor proteins to bring their substrates to the thylakoid membrane.

Cheung CY, Ratcliffe RG, Sweetlove LJ (2015) A method of accounting for enzyme costs in flux balance analysis reveals alternative pathways and metabolite stores in an illuminated Arabidopsis leaf Plant Physiol. http://dx.doi.org/10.1104/pp.15.00880

Lee Sweetlove (Oxford University) leads this study that looks at the Flux Balance Analysis (FBA) of plant metabolism across several metabolic pathways by attaching ‘flux weighting factors’ to allow for the variable intrinsic cost of supporting each flux. This model has been applied to the Arabidopsis leaf exposed to different light regimes to explore the flexibility of the network in meeting its metabolic requirements. The authors discover interesting trade-offs between use of different carbon storage forms and in the variable consumption of ATP and NADPH by different metabolic pathways.

Belfield EJ, Brown C, Gan X, Jiang C, Baban D, Mithani A, Mott R, Ragoussis J, Harberd NP (2014) Microarray-based optimization to detect genomic deletion mutations Genom Data Dec;2:53-54 http://dx.doi.org/10.1016/j.gdata.2014.04.005

GARNet Advisory Board member Nick Harberd (Oxford University) leads this short communication that highlights the development of a tool for detection of genomic deletion mutants in Arabidopsis. Using a NimbleGen whole genome custom tiling array they successfully identify five mutants with deletion ranging from 4bp to 5kb and therefore introduce a powerful tool for analysing this type of genetic lesion in Arabidopsis and other plant species with well-constructed genomes.

Yu C, Liu Y, Zhang A, Su S, Yan A, Huang L, Ali I, Liu Y, Forde BG, Gan Y (2015) MADS-box Transcription Factor OsMADS25 Regulates Root Development through Affection of Nitrate Accumulation in Rice PLoS One http://dx.doi.org/10.1371/journal.pone.0135196

Brian Forde (Lancaster University) is the UK lead on this Chinese collaboration that focuses on nitrate accumulation and how it regulates root development in rice. This occurs via a MADS-box transcription factor OsMADS25 that, when overexpressed in Arabidopsis, promotes primary and lateral root development. Altered expression of this gene also affects root development in transgenic rice and includes significant changes in nitrate accumulation. Therefore this gene might prove to be an important target for future attempts to improve plant growth in regions with altered nitrate concentrations.

page 2 of 2»

Follow Me
TwitterRSS
GARNetweets
December 2019
M T W T F S S
« Nov    
 1
2345678
9101112131415
16171819202122
23242526272829
3031  

Welcome , today is Monday, December 9, 2019