Arabidopsis Research Roundup: December 7th

This weeks Arabidopsis Research Roundup is led by a study from the John Innes Centre in which Lars Ostergaard’s group identify a novel auxin-signaling module. Lars also kindly provides an audio description of this paper where we discuss the significance of this paper for our understanding of auxin signaling.

Secondly is a US-led paper that includes Sabrina Gonzalez-Jorge (University of Cambridge) as a co-author on a study that uses GWAS to identify novel loci involved in amino acid signalling.

Thirdly is a study from Keele University that uses Arabidopsis as an unlikely model for plant silica deposition. Lastly is a paper from the University of Sheffield that focusses on stomatal evolution in land plants.


Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire-Rios A, Sorean K, Weijers D, Friml J, Østergaard L (2016) A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev. 30(20):2286-2296

http://dx.doi.org/10.1101/gad.285361.116 Open Access
Screen Shot 2016-12-07 at 14.36.57
Lars Ostergaard (John Innes Centre) is the corresponding author of this pan-European project that defines a novel auxin-sensing mechanism. Our current understanding of this signaling module revolves around the auxin-mediated degradation of AuxIAA proteins that in turn leads to the derepression of Auxin Response Factor (ARF) transcription factors. This manuscript alters this paradigm by showing that the ARF3/ETTIN protein is able to independently sense auxin through interactions with process-specific transcription factors. This is important for coordinating a diverse range of developmental processes including gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation, whereas disrupting these interactions lead to multiple growth defects. Therefore this manuscript provides insight into a novel mode of auxin signaling that might begin to help explain how auxin can mediate such a broad range of developmental processes.

 


Angelovici R, Batushansky A, Deason N, Gonzalez-Jorge S, Gore MA, Fait A, DellaPenna D (2016) Network-guided GWAS improves identification of genes affecting free amino acids. Plant Physiol. Open Access

Sabrina Gonzalez-Jorge (University of Cambridge) is a co-author on this US-led investigation that used genome-wide association studies (GWAS) techniques to identify new genes that are involved in the production of free amino acids (AAs). These AAs are not only used as protein building blocks but also act as important signaling molecules. In addition, during seed development these free AAs are an important source of energy. By performing GWAS analysis on hundreds of Arabidopsis ecotypes they identify a genomic region that contains two genes of note, namely the cationic amino acid transporter (CAT4) and a polynucleotide phosphorylase resistant to inhibition with fosmidomycin (RIF10). Cat4 mutant plants are deficient in Histidine-related growth processes and given the importance of this amino acid, this region is a prominent candidate for future biofortification strategies. Sabrina Gonzalez-Jorge will be chairing a session at next weeks GARNet Natural Variation Meeting to be held in Cambridge. Look out for the abstract book to be published on the GARNet website at the time of the meeting.
GWASpic


Brugiére T, Exley C (2016) Callose-associated silica deposition in Arabidopsis. J Trace Elem Med Biol. 39:86-90  10.1016/j.jtemb.2016.08.005

This research paper comes from Chris Exley (Keele University) and results from an interest in the mechanism of silica deposition in the common Horsetail and whether this deposition occurs onto template of callose formation. It is known that plant pathogens induce callose deposition so in this study they used Arabidopsis mutants to assess whether induction of leaf callose formation in the presence of silicon could cause silica deposition. Indeed they show that callose deposition is coincident with silica accumulation but not in pmr4 mutant plants, which do not response to pathogen signal. Therefore they show that even though Arabidopsis is not a natural silica accumulator this response can be induced following callose deposition and offers a molecular insight into silicification of plants where this naturally occurs.


Chater CC, Caine RS, Tomek M, Wallace S, Kamisugi Y, Cuming AC, Lang D, MacAlister CA, Casson S, Bergmann DC, Decker EL, Frank W, Gray JE, Fleming A, Reski R, Beerling DJ (2016) Origin and function of stomata in the moss Physcomitrella patens Nat Plants. 2:16179 10.1038/nplants.2016.179

Researchers at the University of Sheffield lead this study in collaboration with colleagues in Leeds, Germany and the USA. They investigate the molecular factors that are required for stomatal development in the model basal land plant Physcomitrella patens. They show that two basic helix-loop-helix proteins PpSMF1 (SPEECH, MUTE and FAMA-like) and PpSCREAM1 (SCRM1) are essential for stomatal formation in moss and their function has been previously shown to rescued by their Arabidopsis orthologs. They show that these proteins function during sporophytic, but not gametophytic, development and in PpSMF1 and PpSCREAM1 mutants the lack of stomata result in delayed dehiscence, suggestive of a role for stomatal signaling in this process in early land plants.

Arabidopsis Research Roundup: November 30th

This weeks Arabidopsis Research Roundup includes an exciting selection of papers that cross a range of subject areas. Firstly is a study led by George Bassel from Birmingham that details cell growth processes across the developing embryo. Secondly Henrik Jonsson at SLCU is a co-author on a study that adds to our understanding of the auxin signaling pathways that controls shoot phyllotaxis. Thirdly are two studies from the University of Oxford that investigate the evolution in land plants of either rooting systems or the response to KNOX transcription factors. Next Cyril Zipfel (TSL) is a co-author on a US-led study that sheds light on the molecular basis of bacterial invasion of the plant apoplast and finally Pierre Petriacq (University of Sheffield) is the lead author of a paper that investigates plant metabolism.

Stamm P, Topham AT, Mukhtar NK, Jackson M, Tome D, Beynon JL, Bassel GW (2016) The transcription factor ATHB5 affects GA-mediated plasticity in hypocotyl cell growth during seed germination. Plant Physiol. http://dx.doi.org/10.1104/pp.16.01099 

Open Access

George Bassel is the corresponding author on this collaboration between the Universities of Birmingham and Warwick. They use 3D single cell analysis to look at the cell shape changes that occur during embryo development and identify two subdomains of cell expansion, the later of which occurs in the embryonic hypocotyl. They find that gibberellic acid (GA) promotes embryo cell expansion and by using single cell network inference, identifedi the transcription factor ATHB5 and its downstream target EXPANSIN3 as key determinants of embryonic hypocotyl extension. Interestingly even though GA-limited conditions lead to reduced hypocotyl growth, embryo development can still occur. This is due to enhanced expansion of the radicle, demonstrating the plastic nature of Arabidopsis embryo development.
Bassellpic


Bhatia N, Bozorg B, Larsson A, Ohno C, Jönsson H, Heisler MG (2016) Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis Curr Biology S0960-9822(16)31128-9 http://dx.doi.org/10.1016/j.cub.2016.09.044

Open Access
MPpic

Henrik Jonsson (SLCU) is a co-author on this study led by Marcus Heisler at EMBL in Heidelberg that looks into the role of auxin during the control of leaf phyllotaxis. In this study they link two well characterized components involved in auxin signaling; the MONOPTEROS (MP) transfcription factor and the PIN1 efflux carrier. PIN1 expression is critical for directing auxin mediated patterning and this is now shown to correspond to patterns of MP expression. When MP expression is perturbed, auxin-generated polarity in the shoot meristem is also affected. They show that MP expression in only the epidermal cell layer is able to promote polarity convergence but that expression in underlying cell layers is critical to anchor these patterns in deeper cell layers. The authors propose that the feedback loop that runs from auxin>MP>PIN1>auxin serves to be a critical component in the generation of plant architectures.


Honkanen S, Jones VA, Morieri G, Champion C, Hetherington AJ, Kelly S, Proust H, Saint-Marcoux D, Prescott H, Dolan L (2016) The Mechanism Forming the Cell Surface of Tip-Growing Rooting Cells Is Conserved among Land Plants. Current Biology http://dx.doi.org/10.1016/j.cub.2016.09.062

Open Access

This manuscript from the lab of Liam Dolan (University of Oxford) continues their work looking at mechanisms that control rooting in a variety of species. On this occasion they show that many aspects of the growth of the rooting system of the liverwort Marchantia polymorpha is controlled by the same orthogroup of genes that function in the development of Arabidopsis root hairs. This importantly demonstrates that constructing the cell surface of tip-growing rooting cells is conserved across evolutionary time.


Frangedakis E, Saint-Marcoux D, Moody LA, Rabbinowitsch E, Langdale JA (2016) Nonreciprocal complementation of KNOX gene function in land plants. New Phytol. http://dx.doi.org/10.1111/nph.14318 Open Access

Jane Langdale (University of Oxford) leads this study into the evolutionary role of Class I KNOTTED-LIKE HOMEOBOX (KNOX) proteins during morphological development in land plants. By performing cross species complementation assays they discovered that, although moss Class I KNOX genes are most similar to those in angiosperms, they are not complemented by an Arabidopsis equivalent. However the converse was not true as the  brevipedicellus (bp-9) mutants can be rescued by the moss PpMKN2 gene. They also show differences in the ability of lycophyte and fern KNOX genes to rescue Arabidopsis mutants. Overall the authors demonstrate that the moss MKN2 protein functions in a broader developmental context than equivalents in other lower plants so they suggest a narrower functional focus evolved following the more recent gene duplications that rescued in the creation of extra KNOX genes.


Xin XF, Nomura K, Aung K, Velásquez AC, Yao J, Boutrot F, Chang JH, Zipfel C, He SY (2016) Bacteria establish an aqueous living space in plants crucial for virulence Nature 539(7630):524-529 http://dx.doi.org/10.1038/nature20166
Bacteriapic
Cyril Zipfel (The Sainsbury Lab, Norwich) is a co-author on this study that is led by researchers in the USA and investigates the molecular basis for the role that high humidity plays in the infectivity of pathogenic bacteria. They show that bacterial infection of the aqueous apoplast requires specific effectors such as Pseudomonas syringae HopM1. The sole addition of this protein is able to transform non-pathogenic into virulent strains under high humidity. Arabidopsis plants deficient in the host target protein that response to HopM1 also exhibit a humidity-dependent phenotype that is a function of the altered homeostasis of the commensal bacteria that make up the complex bacteria interactions within the phyllosphere.


Pétriacq P, De Bont L, Genestout L, Hao J, Laureau C, Florez-Sarasa I, Rzigui T, Queval G, Gilard F, Mauve C, Guérard F, Lamothe-Sibold M, Marion J, Fresneau C, Brown SC, Danon A, Krieger-Liszkay A, Berthomé R, Ribas-Carbo M, Tcherkez GG, Cornic G, Pineau B, Gakiere B, De Paepe R (2016) Photoperiod affects the phenotype of mitochondrial complex I mutants Plant Physiol.

Pierre Petriacq (University of Sheffield) is the lead author on the French-led study that links the role of photoperiod to the plant metabolic engine. Plants with mutants in the mitochondrial Complex I (CI, NADH:ubiquinone oxidoreductase) display a range of phenotypes that also are impacted by photoperiod. The authors show that in two new CI mutant alleles, termed ndufs8.1 and ndufs8.2, grow normally in long days (LD) but show do not response well when moved from SD>LD. Metabolic analysis showed that many parameters are altered in these mutants including altered NAD(H) content. Finally the authors propose that redox homoestasis is linked to the activity of mitochondrial complex and the response to photoperiod.

 

Plants in Computer Vision Meeting: November 16th 2016

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Published on: November 17, 2016

When a PhD student notices that two Arabidopsis rosettes leaves are overlapping, it is trivial for them to measure both. When a researcher is moving through a wheat field trial it is relatively easy to discriminate between different plants from amongst the mass of tissue.

Although straightforward, these approaches are time consuming and are prone to human bias so a broad research goal is to turn this type of imaging over to computer-aided analysis. However, accurately measuring the above examples provides a significant difficulty for computerised imaging systems. The challenge of improving this situation was one of the motivations for the coming together of plant scientists and computer vision (CV) experts at the most recent British Machine Vision Workshop on Plants in Computer Vision, held in London’s Covent Garden.


The day had a broad variety of presentations including those from a plant perspective and those coming from a computer science angle. The 50 delegates were made up of both academics and industry representatives and across subjects from statisticians, engineers, image analysis experts, computer and plant scientists.

One consistently pleasing theme was an excellent attitude of collaboration and sharing. This was exemplified by Andrew French from the Centre for Integrative Biology who introduced the latest iteration of root measurement software termed AutoRoot. This has been prepared in collaboration with Brian Forde at Lancaster University who has developed the microphenotron, which is a high-throughput phenotyping platform. AutoRootAndrew recalled the interesting discussion that occurred during the development of AutoRoot wherein the computer scientists aimed to design software that measured the overall shape of root growth without providing absolute growth values. This was challenging for the plant scientists to accept but was a necessary compromise to enable completely automated computerised imaging. The AutoRoot software will soon be added to the selection of CPIB tools and resources.


Screen Shot 2016-11-17 at 11.30.37
http://phenotiki.com/traits.html

One of the days keynote speakers was Sotorios Tsaftaris, who is now in the department of Engineering at the University of Edinburgh, having spent his career applying computer vision challenges to a variety of imaging tasks. Sotorios’ group has created the affordable PhenoTiki plant phenotyping platform. He has collaborated with plant scientists at the University of Edinburgh to overcome challenges of computer imaging of Arabidopsis genotypes. Look for a paper on this topic imminently. The PhenoTiki system has been designed for imaging of Arabidopsis rosettes and these will be submitted to the BisQue platform running on the CyVerse Collaborative cyber-infrastructure, allowing the remote storage of images.

One of the traits that the PhenoTiki attempts to image is the automated counting of rosette leaves and this topic was also approached by the lab of the meeting chair, Hannah Dee and presented by her colleague Jon Bell. Watching on as a plant scientist, I had never considered how challenging it would be for a computer to differentiate between two overlapping leaves. However this is something that has engaged a lot of research time! Although I didn’t fully understand the CV-basis to their work, they had clearly made some progress with a seemingly straightforward but computationally challenging problem!

JonBellHannahDee


In order to interest other CV labs in the challenges of plant phenotyping, Sotorios Tsaftaris described the open dataset of plant images that he has made freely available for the past year. It is gratifying to hear that 200 people have downloaded the data, the majority of whom are involved in CV research and that the dataset has already been cited in 23 papers! The analysis of the dataset has improved with added successes in the segmenting of rosette images. Sotorios urges other plant scientists to allow full datasets to be released onto this or other websites. This will enable CV researchers to interrogate and to ultimately improve the analysis of this data. Please email datasets@plant-phenotyping.org if you have any interest in donating a dataset for community analysis.


The other keynote speaker, Hanno Scharr from Forschungszentrum Jülich and Rick Van de Zedde from Wagenigen, provided overviews into the remarkable automated facilities that exist on both their sites. Amongst other things, Hanno introduced the PhenoSeeder platform which allows manipulation, measurement and imaging of seeds of all sizes. This has been recently published and although it hasn’t been cheap to develop, it will ultimately enable high-throughout screening of seeds, important both in fundamental science and in the discovery of more beneficial traits. Rick Van de Zedde outlined their PhenomicsNL platform that includes robots that were able to image and then precisely take cuttings from a rose stem for future propagation.

PhenomicsNLThese large scale facilities are going to be critical in the future support for EU plant phenotyping through the EMPHASIS program. On the UK level the Plant Phenotyping centre at Aberystwyth University is a hub for this type of research and includes outstanding research occurring at all levels of plant phenotyping and CV analysis. Please get in contact with them if you have any collaborative ideas.


The final talk of the day was provided by Dr Marco Aita, a trained physicist who has been drawn to plant science by its imaging challenges. He works with Siobhan Braybrook at SLCU on the imaging of the circumnutation response. By using a two-camera setup aligned with CV analysis of the outputs, they have discovered different phases of this response. Currently they are working with wildtype plants but have future plans to look at how different mutants effect this responses. Exciting times ahead! TwoCameraSetup


It is hoped that this meeting will result in a special issue of Plant Methods. The journal’s new editor Tony Pridmore (CPIB) mentioned that they are hoping to accept papers from the CV and imaging communities who have developed tools and methods for analysis of plant growth but that perhaps aren’t yet attached to a biological story. This will hopefully provide an additional route for these tools into use by the general plant science community.

Overall this was an excellent meeting and it was really pleasing to see significant progress since the equivalent gathering in 2015. No doubt this field will continue to grow and hopefully maintain the community-spirit that was evident in this meeting.

Arabidopsis Research Roundup: November 14th

This weeks Arabidopsis Research Roundup is led by a manuscript from Tom Bennett and Ottoline Leyser that looks at Strigolactone signaling for which Tom provides a brief audio description. Elsewhere Verena Kreichbaumer (Oxford Brookes) is a co-author on a study that looks into cytokinin control of auxin biosynthesis and Mike Blatt’s lab at the University of Glasgow continue to elucidate the role of SNARE proteins in vesicle formation. The penultimate paper includes Peter van Esse as a co-author of a study into the role of SERK proteins in the control of different signaling pathways. Finally Pierre Petriacq (University of Sheffield) is the lead-author on a short communication that describes the control of cytosolic calcium by NAD.

Tom Bennett, Yueyang Liang, Madeleine Seale, Sally Ward, Dörte Müller, Ottoline Leyser (2016) Strigolactone regulates shoot development through a core signalling pathway Biology Open http://dx.doi.org/10.1242/bio.021402 Open Access

Tom Bennett is the lead author of this manuscript that results from work conducted in Ottoline Leysers lab at SLCU. Tom has recently started his own lab at the University of Leeds and kindly provides an audio description of this paper that describes their attempts to define determinants of the strigolactone signalling pathway. Initially they define a set of strigolactone responses by assessing multiple aerial phenotypes and show that the degradation of neither BES1 or the DELLA proteins are directly influenced by SCF-MAX2 complex. Importantly they demonstrate that the degradation of SMXL6-related proteins is a key step in strigolactone signalling and that it occurs via the Arabidopsis D14 protein. Finally they show that degradation of SMXL6-related proteins may regulate activity of the BRANCHED1 transcription factor and the PIN-FORMED1 auxin efflux carrier during shoot branching.


Di DW, Wu L, Zhang L, An CW, Zhang TZ, Luo P, Gao HH, Kriechbaumer V, Guo GQ (2016) Functional roles of Arabidopsis CKRC2/YUCCA8 gene and the involvement of PIF4 in the regulation of auxin biosynthesis by cytokinin. Sci Rep. http://dx.doi.org/10.1038/srep36866 Open Access
CKRC2pic
Verena Kreichbaumer (Oxford Brookes University) is a co-author on this paper that aims to tease out the relationship between cytokinin and auxin biosynthesis. They isolate a cytokinin root curling mutant, ckrc2, that is allelic to the YUC8 auxin biosynthetic gene. CKRC2/YUC8 is the rate limiting enzyme in the conversion of indole-2-pyruvic acid to IAA and the gene is induced by cytokinin, a process that requires the transcription factor phytochrome-interacting factor 4 (PIF4). These findings add information to our knowledge of how cytokinin signaling controls auxin biosynthesis.


Zhang B, Karnik R, Waghmare S, Donald NA, Blatt MR (2016) VAMP721 conformations unmask an extended motif for K+ channel binding and gating control. Plant Physiol. http://dx.doi.org/10.1104/pp.16.01549

Open Access

Mike Blatt (University of Glasgow) is the corresponding author on this study that adds to his labs work investigating the factors that control activity of SNARE proteins, which play a major role in intracellular membrane fusion. They show that the VAMP721 protein regulates the function of the KAT1 K+ channel by binding via its SNARE domain, an interaction that opposes VAMP721 binding to the SNARE SYP21.
VAMPpic


van Esse GW, Ten Hove CA, Guzzonato F, van Esse HP, Boekschoten M, Ridder L, Vervoort J, de Vries SC (2016) Transcriptional analysis of serk1 and serk3 receptor-like kinase mutants. Plant Physiol.

This Dutch-led study includes Peter Van Esse from The Sainsbury Lab in Norwich and attempts to decipher the role of Somatic Embryogenesis Receptor like Kinases (SERKs) in brassinosteroid (BR) signalling. They performed a global expression analysis on serk1serk3 double mutant plants and uncovered about 700 differentially regulated genes that, perhaps unsurprisingly, were involved in multiple biological processes. The largest proportion of these genes were either related to BR signalling or primary and secondary metabolism. Furthermore they demonstrated that the serk mutants show some redundancy as many of the serk1serk3 responses are recapitulated in serk3-2 single mutants.


Pétriacq P, Tcherkez G, Gakière B (2016) Pyridine nucleotides induce changes in cytosolic pools of calcium in Arabidopsis. Plant Signal Behav.

http://dx.doi.org/10.1080/15592324.2016.1249082

Pierre Petriacq is a new research fellow at the University of Sheffield and is the lead author of this UK-French-Australian short communication that looks at how the pyridine nucleotide NAD impacts the cytosolic calcium pool. This is a follow up on a recent study that investigated the role of NAD in determination of multiple arms of the plant defence response.

Arabidopsis Research Roundup: November 4th

A couple of weeks of inactivity leads to a bumper edition of the Arabidopsis Research Roundup.
Firstly are two papers from the JIC led by Janelle Balk and Caroline Dean that look at the regulation of the maturation of Fe-S protein complexes or of FLC expression respectively.
Secondly is a study from Liam Dolan in Oxford that looks at regulation of root-hair specific gene expression.
Thirdly is a paper from the University of Bristol that looks at the factors that control the regulation of plastid gene expression.
Fourth are a pair of papers that include work from Phil Wigge’s lab at SLCU that uncover an important mechanism for thermosensing in plants.
Fifth are a set of three papers that look at different aspects of reproductive development from the Universities of Nottingham, Bath or Durham.
Next is a study that includes members of NASC that looks at the transcriptional response to co-predation by two different insects and finally are two studies that focus on work in plants closely related to Arabidopsis thaliana, namely A.Lyrata for a study into the evolution of SI and also the published genome sequence of Cardamine hirsute.

Bastow EL, Bych K, Crack JC, Le Brun NE2, Balk J (2016) NBP35 interacts with DRE2 in the maturation of cytosolic iron-sulfur proteins in Arabidopsis thaliana. Plant J. http://dx.doi.org/10.1111/tpj.13409

Open Access

Janelle Balk (JIC) is the corresponding author on this study that investigates the role of NBP35 in the assembly of Fe-S protein assembly and uncovers its interaction with the DRE2 protein.


Rosa S, Duncan S, Dean C (2016) Mutually exclusive sense-antisense transcription at FLC facilitates environmentally induced gene repression Nat Commun. http://dx.doi.org/10.1038/ncomms13031 Open Access

Caroline Dean (JIC) leads this study that continues her labs analysis of the mechanisms that regulate eukaryotic gene expression focused on the FLC locus. This advance further assesses the role of the COOLAIR antisense transcript on the control of FLC expression.

COOLAIR


 

Vijayakumar P, Datta S, Dolan L (2016) ROOT HAIR DEFECTIVE SIX-LIKE4 (RSL4) promotes root hair elongation by transcriptionally regulating the expression of genes required for cell growth. New Phytologist. http://dx.doi.org/10.1111/nph.14095 Open Access

This paper from the lab of Liam Dolan (University of Oxford) looks at the gene expression network dependent on the role of the ROOT HAIR DEFECTIVE SIX-LIKE4 (RSL4) gene. This reveals genes that are involved in multiple pathways involved in growth including cell signalling and cell wall modifications.


Belbin FE, Noordally ZB, Wetherill SJ, Atkins KA, Franklin KA, Dodd AN (2016) Integration of light and circadian signals that regulate chloroplast transcription by a nuclear-encoded sigma factor New Phytol. http://dx.doi.org/10.1111/nph.14176

Open Access

GARNet committee member Anthony Dodd and colleague Kerry Franklin (University of Bristol) lead this paper that discovers additional aspects of the regulation of nuclear-encoded sigma factor subunit SIG5 that control activity of the plastid-encoded RNA polymerase. They show SIG5 is regulated by an integrated set of light and circadian-mediated signals.


Legris M, Klose C, Burgie ES, Costigliolo C, Neme M, Hiltbrunner A, Wigge PA, Schäfer E, Vierstra RD, Casal JJ (2016) Phytochrome B integrates light and temperature signals in Arabidopsis. Science

http://dx.doi.org/10.1126/science.aaf5656

Jung JH, Domijan M, Klose C, Biswas S, Ezer D, Gao M, Khattak AK, Box MS, Charoensawan V, Cortijo S, Kumar M, Grant A, Locke JC, Schäfer E, Jaeger KE, Wigge PA (2016) Phytochromes function as thermosensors in Arabidopsis. Science. http://dx.doi.org/10.1126/science.aaf6005

These back-to-back papers both include work from Phil Wigge’s lab at the Sainsbury Laboratory in Cambridge. They discover that phytochromeB acts as a thermosensor providing exquisite integration of light and temperature sensing in plants.


Ferguson AC, Pearce S, Band LR, Yang C, Ferjentsikova I, King J, Yuan Z, Zhang D, Wilson ZA (2016) Biphasic regulation of the transcription factor ABORTED MICROSPORES (AMS) is essential for tapetum and pollen development in Arabidopsis. New Phytol.

http://dx.doi.org/10.1111/nph.14200

GARNet committee member Zoe Wilson and colleagues at CPIB in Nottingham collaborate with Chinese researchers to investigate the role of the master regulator ABORTED MICROSPORES in pollen development, mostly through the use of an inducible promotor construct.  n addition they include mathematical modelling of the protein interactions that regulate pollen development.


Wang L, Clarke LA, Eason RJ, Parker CC, Qi B, Scott RJ, Doughty J (2016) PCP-B class pollen coat proteins are key regulators of the hydration checkpoint in Arabidopsis thaliana pollen-stigma interactions New Phytol. http://dx.doi.org/10.1111/nph.14162

Open Access

This study comes from the University of Bath and identifies a novel set of small cysteine-rich proteins (CRPs) that are involved in the pollen-pistil interaction. These proteins are involved in the pollen hydration ‘checkpoint’ that is critical for pollen recognition at the stigma.
Pollen


Campanaro A, Battaglia R, Galbiati M, Sadanandom A, Tonelli C, Conti L (2016) SUMO proteases OTS1 and 2 control filament elongation through a DELLA-dependent mechanism. Plant Reprod. http://dx.doi.org/10.1007/s00497-016-0292-8

This Italian-led study includes Ari Sadanandom (Durham University) as a co-author and builds upon past work in this lab that has looked at the role of the OTS SUMO proteases. This paper shows that OTS1 and OTS2 are involved in stamen elongation in a response that overlaps with GA signaling.


Kroes A, Broekgaarden C, Castellanos Uribe M, May S, van Loon JJ, Dicke M (2016) Brevicoryne brassicae aphids interfere with transcriptome responses of Arabidopsis thaliana to feeding by Plutella xylostella caterpillars in a density-dependent manner Oecologia. http://dx.doi.org/10.1007/s00442-016-3758-3

Open Access

Two members of NASC, including GARNet committee member Sean May, are co-authors on this German-led study that investigates how the relationship between aphid and caterpillars effects the Arabidopsis transcriptome. They show that the response to caterpillars was altered by additional aphid predation, which was also dependent on aphid density.


Mable BK, Hagmann J, Kim ST, Adam A, Kilbride E, Weigel D, Stift M (2016) What causes mating system shifts in plants? Arabidopsis lyrata as a case study. Heredity http://dx.doi.org/10.1038/hdy.2016.99

Members of Mark Stift’s lab group, which used to be at the University of Glasgow, are included in this German-led study that uses Arabidopsis lyrata to investigate the factors that contribute to the genetic breakdown of self-incompatibility (SI).


Gan X, Hay A, Kwantes M, Haberer G, Hallab A, Ioio RD, Hofhuis H, Pieper B, Cartolano M, Neumann U, Nikolov LA, Song B, Hajheidari M, Briskine R, Kougioumoutzi E, Vlad D, Broholm S, Hein J, Meksem K, Lightfoot D, Shimizu KK, Shimizu-Inatsugi R, Imprialou M,Kudrna D, Wing R, Sato S, Huijser P, Filatov D, Mayer KF, Mott R, Tsiantis M (2016) The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nature Plants. http://dx.doi.org/10.1038/nplants.2016.167

This publication of the Cardamine hirsuita genome is led by Miltos Tsiantis and includes participants from University of Oxford and UCL. They demonstrate specific roles for Cardamine proteins in leaf diversity and seed pod shatter.

Plants at iGEM2016

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Published on: November 3, 2016

As even the name suggests, the iGEM Giant Jamboree is a conference like no other.

iGEM_Above
Photo credit: the iGEM Foundation and Justin Knight

Consider that there are 2500 mostly undergraduate students from all around the world, the vast majority of them at their first conference and each giving presentations that are being critically assessed. This provides a clue as to the kind of frenetic and excited energy that characterises this event.

For those a little confused, the International Genetically Engineered Machine Foundation oversees and organizes iGEM, which is synthetic biology competition for groups of participants who are usually hosted by academic institutions. The basic idea is that a group of students works through the summer on a completely novel project that conforms to the principles of synthetic biology, before presenting it in the aforementioned Giant Jamboree.

As this is a competition, each project is judged on metrics that assess many aspects of the teams work. These include the contribution of biobricks to the iGEM registry (an impressive selection of molecular parts that are held within a standardised plasmid), the development of their novel project, initiating collaborations with other teams and their attempts to integrate human practices and public engagement into their project. By meeting certain criteria each team is eligible for Gold, Silver or Bronze medals alongside special prizes for different project categories.

Given registrations, student stipends, research expenses, travel and accommodation, putting forward even a small team can stretch to at least £20K. Therefore this is not a something to be taken lightly. To this financial requirement must be added the time donated by a team of instructors and advisors that support the students. However regardless of the cost, one thing is certain; for those students who participate, attend, present and are inspired by the Jamboree, it can be a career-defining moment.


 

Plant Synthetic Biology can make for a challenging summer!

Plant experimental chassis have not been widely used during the ten years of the iGEM competition where bacteria, yeast, mammalian cell lines or cell-free systems offer time efficient alternatives for the usual 10-week research period. However the iGEM foundation, alongside a group of committed advocates have recently developed the Phytobricks cloning standard, which is based on a recently published standard syntax within the Golden Gate cloning system. The aim is to lower the barrier of accessibility for teams to start plant projects and the evidence from this years competition seems to suggest that this is slowly happening.
T--Valencia_UPV--HYPE-IT-workflow
The 2016 iGEM team from Valencia-UPV is advised by plant synthetic biologist Diego Orzaez and their project submitted phytobricks for the expression of a split Cas9 system. They showed that the two halves of the Cas9 protein could reconstitute and was active in a tobacco expression system. They have documented this work on their Parts pages and this is hopefully a resource that will be used by future iGEM teams. Their team was very successful at the jamboree, winning a gold medal alongside specific awards for the best hardware  and software.

Another successful team with a plant project was from SCAU-China who had, over the course of at least two years, added an additional two genes to conventional Golden rice.
This produces a ‘brown rice’ that produces the natural keto-carotenoid Astaxanthin, which is thought to have beneficial anti-oxidant properties. This is clearly a significant research project that has been badged with the iGEM logo and as such was very positively received by the judges. Although they did not submit parts in the Phytobricks standard it was exciting to see such a potentially high profile plant-project feature at the jamboree.
T--SCAU-China--Demonstrate1  These projects are well deserving of their awards and their work builds upon years of expertise contained within the supporting labs. This highlights one of the challenges for the competitive element of iGEM; namely how teams can be equally judged when they have hugely varying levels of support. Fortunately it appears that this is not a significant issue as each team is able to take positives from their own performances and are happy to celebrate the excellent projects that they each had individually put together.

Remarkably the iGEM competition includes at least 30 high school teams and one of these, GDSYZX in China, worked with plant light responsive promoters that they added to the Parts Registry.


Algae on the rise.

A number of teams including Cambridge-JIC, Linkoping University in Sweden and USP_UNIFESP in Brazil used the algae Chlamydomonas_reinhardtii in their projects. Cambridge team had most success in their project that generated a set of parts in the Phytobrick standard that can be used in future algal projects. In addition they created a remarkable blueprint for the production of a prototype Genegun for plant transformation, costing just £300, making it accessible for less well funded labs. The other two teams mentioned above were hoping to use Chlamydomonas to produce either biofuels or spider silk protein and although the ambition of both projects outstripped their achievements this year, iGEM is all about thinking big: sometimes it works, sometimes not!

Screen Shot 2016-11-03 at 10.59.29The team from Pretoria in South Africa took on an extremely ambitious plan called WattsApatmer to create ‘plant batteries’ by using short aptamers to attach either photosystem II or a laccase enzyme to either pole of an electrical circuit held within a novel graphene scaffold. The students made some progress with this and the project serves to highlight the blue-sky thinking that undergraduate students undertake as part of this competition.
T--Pretoria_UP--WattsAptamer_Project_Design It is clearly difficult to make enormous progress over a summer project but there were so many amazing project ideas on display at this iGEM I hope that the host institutions can find finances to develop some of these ideas so that some can come to fruition to add value to the time already committed to these projects.


Europe on Top

From a UK and European perspective the iGEM jamboree was a huge success with Imperial College and LMU TU Munich taking the overall undergrad and overgrad awards respectively, with remarkable projects that highlighted the talent of their students and the level of support their receive from their host institutions.

The UK was represented by over 20 teams, the third most numerous behind the USA and China. Aside from Imperial College, the teams from Exeter, Dundee, Dundee Schools, Cambridge-JIC, Oxford, Sheffield, UCL, Glasgow and Manchester gained Gold medals. There is little doubt that the UK is developing a cohort of talented synthetic biologists who will be the research leaders of the future.

Overall we look forward to seeing the number of plant projects increase over the years to come. The development of the Phytobrick standard will undoubtedly help in this goal for students to come up with ideas to test the possibility of using plants in their projects.

There are exciting times ahead for plant synthetic biology!

Arabidopsis Research Roundup: October 21st

This weeks Roundup demonstrates a wide breadth of research topics that use Arabidopsis as the model organism. Firstly Matthew Terry and colleagues investigate the factors that control reterograde signaling between chloroplast and nucleus. Secondly researchers from the University of Sheffield demonstrate that a component of the cell wall is involved in stomatal opening. Thirdly Malcolm Bennett and Ranjan Swarup from CPIB are co-authors on research that touches on a familiar topic, the regulation of the AUX1 protein in Arabidopsis roots. Fourthly Alastair Rutherford is a collaborator on a US-led study that investigates the proton motion force across thylakoid membranes. Finally are two studies wherein UK academics, namely David Salt and Malcolm Hawkesford, are co-authors on German-led studies that investigate a plants response to different minerals.

Page MT, McCormac AC, Smith AG, Terry MJ (2016) Singlet oxygen initiates a plastid signal controlling photosynthetic gene expression. New Phytol.

http://dx.doi.org/10.1111/nph.14223

Open Access
HaemPic
Matthew Terry (Southampton) is the lead author on this study that investigates the factors regulating retrograde signaling between chloroplast and nucleus. One model for the control of this process is based around a signal, which is abolished by the herbicide norflurazon, which is related to levels of haem in chloroplasts. In addition this reterograde signalling can be damaged by the transfer of seedlings from far-red to white light. This study investigates whether these external factors influence the same endogenous signal transduction pathway and show, perhaps surprisingly, that different sets of genes are mostly affected in each case. FR pretreatment results in the damaging production of singlet oxygen molecules, which is inhibited by a mutant that lacks a correct signaling pathway that responds to oxygen. The authors suggest that this control process, wherein the production of oxygen in the chloroplast is a signal for reduced photosynthetic gene expression, acts to fine tune this system in response to differing light conditions.

 

Amsbury S, Hunt L, Elhaddad N, Baillie A, Lundgren M, Verhertbruggen Y, Scheller HV, Knox JP, Fleming AJ, Gray JE (2016) Stomatal Function Requires Pectin De-methyl-esterification of the Guard Cell Wall. Current Biology

http://dx.doi.org/10.1016/j.cub.2016.08.021

Open Access
Gray_Pic
This manuscript is led by Julie Gray and Andrew Fleming at the University of Sheffield and looks at how the composition of the plant cell wall can affect stomatal opening. They show that guard cell walls are rich in un-esterified pectins and that a pectin methylesterase gene, PME6, is required for stomatal function and appropriately is highly expressed in this tissue. Mutant pme6 plants have an altered cell wall composition alongside a reduction in the dynamics of stomatal opening, indicating that there is a mechanical constraint on the ability of their guard cell walls to move in an appropriate manner. Overall, pme6 plants show decreased growth, due to increased CO2 loss, a phenotype that can be rescued by growth in elevated CO2. Although it is well known that multiple signals converge to control stomatal movement, this manuscript introduces a downstream component to this pathway that links in the physical movement of the guard cell walls.

 

Street IH, Mathews DE, Yamburkenko MV, Sorooshzadeh A, John RT, Swarup R, Bennett MJ, Kieber JJ, Schaller GE (2016) Cytokinin acts through the auxin influx carrier AUX1 to regulate cell elongation in the root. Development http://dx.doi.org/10.1242/dev.132035

This paper features Malcolm Bennett and Ranjan Swarup from CPIB as co-authors on a paper led by US colleagues. The requirement for hormone crosstalk has long been known to be critical for the precise control of root development. This study shows the role of cytokinin in modulation of auxin activity in the lateral root cap is dependent on the auxin influx carrier AUX1. This is true of ethylene dependent and independent modes of cytokinin action. Furthermore an autoregulatory signalling loop is discovered that integrates the effects of cytokinin and auxin and features AUX1 as well as the auxin responsive transcription factor ARR10. This study adds further detail to our knowledge of the mechanisms by which cytokinin controls root growth via auxin transport.

 

Davis GA,, Kanazawa A,, Schöttler MA, Kohzuma K, Froehlich JE, Rutherford AW, Satoh-Cruz M, Minhas D, Tietz S, Dhingra A, Kramer DM (2016) Limitations to photosynthesis by proton motive force-induced photosystem II photodamage. Elife

http://dx.doi.org/10.7554/eLife.16921

Open Access

Alastair Rutherford (Imperial College) is a co-author on this study that is led by researchers at Michigan State. They use a range of Arabidopsis mutants that show altered thylakoid lumen proton efflux to investigate their effect on the thylakoid proton motive force (pmf). PMF is required for the production of ATP and concomitantly could be considered essential for life on Earth. These mutants show alterations in photosynthetic regulation as well as on levels of photosystem II photodamage. More detailed measurements show that these phenotypes are dependent on an elevated electric field across the thylakoid, which alters the activity of PSII and its subsequent photodamage through production of destructive oxygen species. This alteration in the electric field across the thylakoid is important in wildtype plants and the authors suggest that the photodamage that naturally occurs in fluctuating light conditions could represent a limiting factor for plant productivity.

 

Kühnlenz T, Hofmann C, Uraguchi S, Schmidt H, Schempp S, Weber M, Lahner B, Salt DE, Clemens S (2016) Phytochelatin Synthesis Promotes Leaf Zn Accumulation of Arabidopsis thaliana Plants Grown in Soil with Adequate Zn Supply and is Essential for Survival on Zn-contaminated Soil. Plant Cell Physiol.

http://dx.doi.org/10.1093/pcp/pcw148

Open Access
Zn_Pic
Current GARNet Chairman and a recent arrival at CPIB in Nottingham, David Salt is a co-author on this German-led paper that assesses the role of Phytochelatin (PC) on plant growth in zinc contaiminated soils. PC is known to be essential for metal detoxification yet its role in zinc tolerance is not fully appreciated. Therefore wildtype and PC mutant (atpcs1) Arabidopsis were grown in soil with varying zinc concentrations. High concentrations of zinc cause PC upregulation, a response that is significantly compromised in atpcs1 mutant plants. Interestingly mutant plants show differing zinc levels when compared to wildtype in either normal or zinc-limited conditions. Finally the authors dissect the regulatory elements within AtPCS1 protein, showing that there are distinct domains that are responsible for activation by zinc or cadmium. This is indicative of a level of differential activity and is suggestive of the presence of multiple signaling pathways to deal with metal accumulation.

Forieri I, Sticht C, Reichelt M, Gretz N, Hawkesford MJ, Malagoli M, Wirtz M, Hell R (2016) Systems analysis of metabolism and the transcriptome in Arabidopsis thaliana roots reveals differential co-regulation upon iron, sulfur and potassium deficiency. Plant Cell Environ. http://dx.doi.org/10.1111/pce.12842

Open Access

This German-led study includes Malcolm Hawkesford (Rothamstead Research) and investigates shoot growth under iron, potassium or sulfur deficiency. When these minerals were adjusted to cause equivalent alterations in shoot growth they showed specific morphological alterations, changes in root metabolic profiles and in transcriptional responses. Iron deficiency causes the strongest gene expression changes, altering up to 18% of the transcriptome. A surprisingly small number of genes (180) were co-regulated by all of the nutrients. Iron deficiency alters a different set of genes involved in sulfur regulation compared to those observed in conditions of sulfur deficiency itself, indicative of mineral-specific cross-regulation of response pathways. Overall these experiments enable the dissection of general stress responses from those induced by specific deficiencies at the metabolic and transcriptomic scales.

Arabidopsis Research Roundup: October 6th.

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Published on: October 6, 2016

This week Arabidopsis Research Roundup includes an audio description from Robert Sablowski about work from this lab that describes the early specification of stem tissue within the shoot apical meristem. In addition multiple members of CPIB in Nottingham are involved in two connected papers that describe how auxin homeostasis is controlled at the cell and tissue level. Researchers from the University of Bristol shed light on the relationship between viral infection and stomatal development whilst Claudius Marondedze from the University of Cambridge in involved in a study that has used next generation lighting technology to grow Arabidopsis. Finally Sean May from NASC is a co-author on a study that looks into the role of brassinosteroid on the response to freezing temperatures.

Bencivenga S, Serrano-Mislata A, Bush M, Fox S, Sablowski R (2016) Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis. Dev Cell. S1534-5807(16)30588-3

http://dx.doi.org/10.1016/j.devcel.2016.08.013 Open Access

Robert Sablowski (John Innes Centre) is the lead author on this study that investigates the origin of Arabidopsis stem tissue within the shoot apical meristem (SAM). They show that the transcription factor REPLUMLESS (RPL) is responsible for patterning in the central and peripheral regions of the Rib Zone, which is a subset of cells within the SAM. The authors identify genes that are targeted by RPL, including LIGHT-SENSITIVE HYPOCOTYL 4 that had been previously identified as an organ boundary gene and in this context is involved in the same signaling pathway as RPL. This work opens up new avenues to research stem development, which is a critical yet little studied aspect of plant growth.

Professor Sablowski kindly provides an audio description of this work.

On an additional note, last year Robert collaborated with Maddie Moate to produce an excellent video about meristems!


Porco S, Pěnčík A, Rashed A, Voß U, Casanova-Sáez R, Bishopp A, Golebiowska A, Bhosale R, Swarup R, Swarup K, Peňáková P, Novák O, Staswick P, Hedden P, Phillips AL, Vissenberg K, Bennett MJ, Ljung K (2016) Dioxygenase-encoding AtDAO1 gene controls IAA oxidation and homeostasis in Arabidopsis. PNAS

http://dx.doi.org/10.1073/pnas.1604375113 Open Access

Mellor N, Band LR, Pěnčík A, Novák O, Rashed A, Holman T, Wilson MH, Voß U, Bishopp A, King JR, Ljung K, Bennett MJ, Owen MR (2016) Dynamic regulation of auxin oxidase and conjugating enzymes AtDAO1 and GH3 modulates auxin homeostasis. PANS

http://dx.doi.org/ 10.1073/pnas.1604458113 Open AccessDAO1pic

Malcolm Bennett and colleagues at CPIB in Nottingham are authors on back-to-back manuscripts in PNAS that investigate the control of auxin metabolism and homeostasis. Both papers focus on the role of the DIOXYGENASE FOR AUXIN OXIDATION 1 (AtDAO1) gene in this process. AtDAO1 is a highly expressed IAA oxidase that, when disrupted, causes significant changes in the steady state levels of oxIAA and IAA conjugates, but not IAA itself, which may explain why the atdao1 mutant has a relatively mild phenotype. AtDAO1, along with the GH3 IAA-conjugating enzymes are auxin-inducible, demonstrating that these proteins play a role in auxin homeostasis that is dependent on the prevailing auxin concentration.

The second paper develops a mathematical model for the interactions between AtDAO1, the GH3 enzymes, the relationship between auxin biosynthesis and conjugation and how these changes occur at different auxin concentrations. In addition they extend this homeostasis model into a multicellular environment demonstrating that the role of AtDAO1 differs across root tissues in a manner that is predicted by the mutant phenotype.


Murray RR, Emblow MS, Hetherington AM, Foster GD (2016) Plant virus infections control stomatal development. Sci Rep.

http://dx.doi.org/10.1038/srep34507 Open Access

Gary Foster and Alistair Hetherington at the University of Bristol are the lead authors on this study that demonstrates that plant viral infections affect stomatal development in both Nicotiana tabacum and Arabidopsis thaliana. In both cases susceptible, but not resistant, plants showed a lower stomatal index (stomatal density / stomatal density+epidermal cell density) whilst the stomatal density was reduced in susceptible Arabidopsis plants. This preliminary study provides evidence for a relationship between viral infection and stomatal development that will undoubtedly lead to many other studies on this topic.


Ooi A, Wong A, Ng TK, Marondedze C, Gehring C, Ooi BS (2016) Growth and development of Arabidopsis thaliana under single-wavelength red and blue laser light. Sci Rep

http://dx.doi.org/10.1038/srep33885 Open Access

This Saudi-Arabia based study includes Claudius Marondedze from the University of Cambridge and uses Arabidopsis as a model to understand mechanisms of growth that are important in the development of indoor horticulture. These experiments involve growing Arabidopsis under high-powered single-wavelength lasers and show that they grow normally from seed to seed. The authors perform a proteomic analysis and show that these plants have lower expression of proteins involved in light and radiation stress. Therefore this study offers an insight into the potential of using this next generation lighting technology for future horticultural applications.


Eremina M, Unterholzner SJ, Rathnayake AI, Castellanos M, Khan M, Kugler KG, May ST, Mayer KF, Rozhon W, Poppenberger B (2016) Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants. PNAS

http://dx.doi.org/10.1073/pnas.1611477113

This German-led study includes GARNet Committee member and NASC Director Sean May and looks into the role of brassinosteroids in the control of freezing tolerance in Arabidopsis. BR-response mutants are hypersensitive to freezing while constitutive BR signaling provides enhanced freezing tolerance. This study shows that this BR effect is mediated via well-known C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR (CBF) proteins but also through CBF-independent signaling. Finally the authors provide a model to explain the role of BR during the response to freezing stress. BRpic

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