GARNet Research Roundup: July 26th 2019

This summer-time-reading bumper edition of the GARNet Research Roundup begins with two papers from the University of Sheffield that each use advanced imaging techniques. Firstly Andrew Fleming’s group leads a study on the link between stomatal function and mesophyll space morphology. Second is a study from Matthew Johnson’s group that looks at the dynamic arrangement of thylakoid stacks.

Next are two papers that include Alison Smith from the JIC as a corresponding author. The first also includes Vasilios Andriotis from the University of Newcastle and looks at the role of the plastidial pentose phosphate pathway during post-germination growth. Second uses a gene-editing strategy to generate potatoes with altered starch morphologies.

The fifth paper also looks at starch; researchers from Cambridge and Norwich are involved in a study that characterises the role of the LIKE SEX4 1 protein in starch degradation.

The sixth paper is from Aberystwyth University and identifies a transcription factor that alters secondary cell wall composition in Brachypodium and maize. Next is research from the University of Bath that looks at the role of a protein S-acyl transferase during seed germination.

The eighth and ninth papers are led by Spanish research groups and include contributions from UK-based co-authors in Cambridge and Nottingham, working on photoperiod perception or phosphate signaling respectively.

The tenth paper features work from Cardiff University and looks at the role of heterologous expression of the Arabidopsis WEE1 protein. The Bancroft lab from the University of York leads the next paper that investigates glucosinolate signaling in Brassica napus.

The final three manuscripts are methods papers. The first from Edinburgh introduces a new NanoLUC reporter whilst the other two include techniques involved in the investigation of light-regulated growth processes.


Lundgren MR, Mathers A, Baillie AL, Dunn J, Wilson MJ, Hunt L, Pajor R, Fradera-Soler M, Rolfe S, Osborne CP, Sturrock CJ, Gray JE, Mooney SJ, Fleming AJ (2019) Mesophyll porosity is modulated by the presence of functional stomata. Nat Commun. doi: 10.1038/s41467-019-10826-5

Open Access

This UK-wide study is led from Andrew Fleming’s lab in Sheffield and includes Marjorie Lundgren as first author (now working in Lancaster). They use microCT imaging alongside more traditional measurements linked to analysis of gas exchange to show that mesophyll airspace formation is linked to stomatal function in both Arabidopsis and wheat. This allows the authors to propose that coordination of stomata and mesophyll airspace pattern underpins water use efficiency in crops.

https://www.nature.com/articles/s41467-019-10826-5

Wood WH, Barnett SFH, Flannery S, Hunter CN, Johnson MP (2019) Dynamic thylakoid stacking is regulated by LHCII phosphorylation but not its interaction with photosystem I. Plant Physiol. doi: 10.1104/pp.19.00503

Open Access

William Wood is the first author on this study from the University of Sheffield that uses 3D structured illumination microscopy (3D-SIM) to look at the dynamics of thylakoid stacking in both Arabidopsis and spinach. They show that the processes they observe are dependent on light harvesting complex II phosphorylation.

http://www.plantphysiol.org/content/early/2019/06/11/pp.19.00503.long

Andriotis VME, Smith AM (2019) The plastidial pentose phosphate pathway is essential for postglobular embryo development in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1908556116

Open Access

Vasilios Andriotis (now at the University of Newcastle) is the lead author of this work performed in Alison Smith’s lab at the JIC. They look at the role of the plastidial oxidative pentose phosphate pathway (OPPP) during embryo development. This involved demonstrating that production of ribose-5-phosphate (R5P), which in turn leads to synthesis of purine nucleotides, is a critical function of the OPPP.


Tuncel A, Corbin KR, Ahn-Jarvis J, Harris S, Hawkins E, Smedley MA, Harwood W, Warren FJ, Patron NJ, Smith AM (2019) Cas9-mediated mutagenesis of potato starch-branching enzymes generates a range of tuber starch phenotypes. Plant Biotechnol J. doi: 10.1111/pbi.13137

Open Access

Alison Smith and Nicola Patron who work in Norwich Research Park are corresponding authors of this study that includes Aytug Tuncel as first author. They have used Cas9-mediated gene editing to generate potato plants that have a range of different tuber starch structures. This shows that gene-editing techniques allows the transgene-free alteration to generate potentially healthier crops.


Schreier TB, Umhang M, Lee SK, Lue WL, Shen Z, Silver D, Graf A, Müller A, Eicke S, Stadler M, Seung D, Bischof S, Briggs SP, Kötting O, Moorhead GB, Chen J, Zeeman SC (2019) LIKE SEX4 1 acts as a β-amylase-binding scaffold on starch granules during starch degradation. Plant Cell. doi: 10.1105/tpc.19.00089

Open Access

Tina Schreier from the University of Cambridge is the first author on this international study led from Switzerland that also includes Alexander Graf and David Seung from the JIC as co-authors. This study defines a precise role for the LIKE SEX FOUR 1 (LSF1) protein that binds starch and is required for normal starch degradation. Through a variety of experiments they show that the glucan binding, rather than phosphatase activity, is required for LSF1 function during starch degradation.


Bhatia R, Dalton S, Roberts LA, Moron-Garcia OM, Iacono R, Kosik O, Gallagher JA, Bosch M (2019) Modified expression of ZmMYB167 in Brachypodium distachyon and Zea mays leads to increased cell wall lignin and phenolic content. Sci Rep. doi: 10.1038/s41598-019-45225-9

Open Access

Rakesh Bhatia is the first author on this work from the lab of Maurice Bosch at Aberystwyth University. They overexpress the maize MYB transcription factor ZmMYB167 in both Brachypodium and maize. Both species show increased lignin content with Brachypodium but not maize showing a biomass deficit. This indicates that ZmMYB167 could be a useful molecular tool for the alteration of secondary cell wall biosynthesis.

https://www.nature.com/articles/s41598-019-45225-9

Li Y, Xu J, Li G, Wan S, Batistic O, Sun M, Zhang Y, Scott R, Qi B (2019) Protein S-acyl Transferase 15 is Involved in Seed Triacylglycerol Catabolism during Early Seedling Growth in Arabidopsis (2019) J Exp Bot. doi: 10.1093/jxb/erz282

First author on this UK-Chinese collaboration is Yaxiao Li who works with Baoxiu Qi at the University of Bath. The authors characterise the function of Arabidopsis Protein Acyl Transferase 15, AtPAT15. This protein is involved in essential β-oxidation of triacylglycerols during post-germination growth.


Ramos-Sánchez JM, Triozzi PM, Alique D, Geng F, Gao M, Jaeger KE, Wigge PA, Allona I, Perales M (2019) LHY2 Integrates Night-Length Information to Determine Timing of Poplar Photoperiodic Growth. Curr Biol. doi: 10.1016/j.cub.2019.06.003

Open Access

This Spanish-led study includes co-authors from the Sainsbury Laboratory in Cambridge and attempts to define the factors that control photoperiod perception in trees, using poplar as a model system. FLOWERING LOCUS T2 (FT2) has been previously shown to be involved in this process and this study builds on that work to show that night-length information is transmitted by the clock gene LATE ELONGATED HYPOCOTYL 2 (LHY2) and is able to control FT2 expression.

https://www.cell.com/current-biology/fulltext/S0960-9822(19)30696-7?

Silva-Navas J, Conesa CM, Saez A, Navarro-Neila S, Garcia-Mina JM, Zamarreño AM, Baigorri R, Swarup R, Del Pozo JC (2019) Role of cis-zeatin in root responses to phosphate starvation. New Phytol. doi: 10.1111/nph.16020

Ranjan Swarup from the University of Nottingham is a co-author on this Spanish-led study that has Javier Silva-Navas as first author. Through analysis of dark-grown seedlings they have identified a set of new genes involved in root phosphate signaling. In addition they provide evidence of a links between cytokinin and phosphate signaling through modulation of the cell cycle.


Siciliano I, Lentz Grønlund A, Ševčíková H, Spadafora ND, Rafiei G, Francis D, Herbert RJ, Bitonti MB, Rogers HJ, Lipavská H (2019) Expression of Arabidopsis WEE1 in tobacco induces unexpected morphological and developmental changes. Sci Rep. 2019 Jun 18;9(1):8695. doi: 10.1038/s41598-019-45015-3

Open Access

Ilario Siciliano leads this work that includes colleagues from Hilary Rogers’ lab at Cardiff University. The WEE1 protein regulates the cell cycle across eukaryote lineages. In this work they show that overexpression of AtWEE1 in tobacco causes precocious flowering and increased shoot morphogenesis of stem explants whilst in cell culture this WEE1 OX causes smaller cell sizes.


Kittipol V, He Z, Wang L, Doheny-Adams T, Langer S, Bancroft I (2019) Genetic architecture of glucosinolate variation in Brassica napus. J Plant Physiol. doi: 10.1016/j.jplph.2019.06.001

Open Access

This study from the Bancroft lab at the University of York is led by Varanya Kittipol. Through use of Associative Transcriptomics (AT) across a diversity panel of 288 Brassica napus genotypes they are able to identify a set of genes involved in synthesis of glucosinate hydrolysis products.


Urquiza-García U, Millar AJ (2019). Expanding the bioluminescent reporter toolkit for plant science with NanoLUC. Plant Methods. doi: 10.1186/s13007-019-0454-4

Open Access

This study from the University of Edinburgh introduces NanoLUC, a new more stable luciferase-based reporter for use by the plant community.

The final two papers are methods papers that focus on different aspects of light-regulated growth. These are from the University of Southampton and University of York.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0454-4

Terry MJ, Kacprzak SM (2019) A Simple Method for Quantification of Protochlorophyllide in Etiolated Arabidopsis Seedlings. Methods Mol Biol. doi: 10.1007/978-1-4939-9612-4_14

Oakenfull RJ, Ronald J, Davis SJ (2019) Measuring Phytochrome-Dependent Light Input to the Plant Circadian Clock. Methods Mol Biol. doi: 10.1007/978-1-4939-9612-4_15

Arabidopsis Research Roundup: November 1st.

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Published on: November 1, 2017

This weeks Research Roundup includes three research and two methods papers. Firstly is work from the O’Connor and Leyser groups at SLCU that investigates the diversity of function in PIN auxin transporters between monocots and dicots. Secondly research from the Kover lab at the University of Bath has characterised the photosynthetic contribution of the inflorescence stem whilst the third paper is from the Bill Finch-Savage at the University of Warwick and looks at the effect of temperature on seed dormancy. Finally are two methods paper from the University of Warwick and Leeds that introduce protocols for the imaging of either the endoplasmic reticulum or the ultrastructure of pollen tubes.


O’Connor DL, Elton S, Ticchiarelli F, Hsia MM, Vogel JP, Leyser O (2017) Cross-species functional diversity within the PIN auxin efflux protein family. Elife. doi: 10.7554/eLife.31804

Open Access

Devin O’Connor and Ottoline Leyser (SLCU) lead this research that bridges the divide between a model dicot (Arabidopsis) and a model monocot (Brachypodium)as they investigate mechanisms of auxin transport, focussed on the PIN protein family. Arabidopsis lacks a clade of PIN proteins (termed Sister-of-PIN1 (SoPIN1) that are found in other plant species. They show that Brachypodium sopin1 mutants have inflorescence defects similar to Arabidopsis pin1 mutants, a similarity of function that is confirmed by the ability of soPIN1 to rescue the phenotype of null Atpin1 plants. However Brachy PIN1 is only able to rescue a less severe Atpin1 mutant. Overall they demonstrate that PIN1 functional specificity is determined by membrane and tissue-level accumulation and transport activity. As this paper is published in Elife, the journal provides reviewer comments and in this case they show that this manuscript was initially rejected. However the authors persisted and provided a reworked manuscript that convincing the reviewers that this study was appropriate for publication in Elife. An excellent lesson in persistence!


Gnan S, Marsh T, Kover PX (2017) Inflorescence photosynthetic contribution to fitness releases Arabidopsis thaliana plants from trade-off constraints on early flowering PLoS One doi: 10.1371/journal.pone.0185835

Open Access

In this study from Paula Kover’s lab at the University of Bath they investigate how the photosynthetic capacity of the Arabidopsis influoresence influences the time of flowering in a range of accessions. Interestingly after plants had flowering the authors removed rosette leaves to assess the ability of the influoresence to support future plant growth. Surprisingly there was a wide variation in general fitness following leaf removal, ranging from a growth reduction of 65% to no observed loss in fitness. These changes are due to both the differencies in the flowering time and in the number of lateral branches. This can explain how early flowering accessions can maintain fitness despite reduced vegetative growth.


Huang Z, Footitt S, Tang A, Finch-Savage WE (2017) Predicted global warming scenarios impact on the mother plant to alter seed dormancy and germination behavior in Arabidopsis Plant Cell Environ. doi: 10.1111/pce.13082

William Finch-Savage (University of Warwick) leads this investigation into the effect of temperature on seed development and dormancy. They used specially designed polyethylene tunnels that allowed in vivo variations in temperature and light conditions. Perhaps unsurprisingly they showed that temperature plays a significant role in future seed development with lower temperatures promoting dormancy but higher temperatures reduced dormancy that subsequently alters the timing of future life cycles, which has consequences for the species fitness.


Dzimitrowicz N, Breeze E, Frigerio L (2018) Long-Term Imaging of Endoplasmic Reticulum Morphology in Embryos During Seed Germination. Methods Mol Biol. doi: 10.1007/978-1-4939-7389-7_6

Lorenzo Frigerio (University of Warwick) leads this methods paper that describes the imaging of the endoplasmic reticulum over long periods during seed germination.


Ndinyanka Fabrice T, Kaech A, Barmettler G, Eichenberger C, Knox JP, Grossniklaus U, Ringli C (2017) Efficient preparation of Arabidopsis pollen tubes for ultrastructural analysis using chemical and cryo-fixation. BMC Plant Biol. doi: 10.1186/s12870-017-1136-x

Paul Knox (University of Leeds) is a co-author on this methods paper that outlines the necessary steps for efficient preparation of pollen tubes for subsequent ultrastructural analysis.

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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