GARNet Research Roundup: Jan 24th 2020

The first GARNet Research Roundup of 2020 begins with a study from the University of Dundee at the James Hutton Institute in which they have adapted nanopore direct sequencing to analyse the Arabidopsis mRNA methylome. The second study is also from Dundee and is an analysis of alternative splicing in C4 sugarcane.

The next two papers look at the control of stomatal development. In the first, researchers from Bristol investigate the integration of temperature and light-induced signals whilst the second paper is from Sheffield and looks at the role, or lack thereof, of the HY5 protein. The fifth paper is also from Sheffield and looks at the role of the MALECTIN DOMAIN KINESIN 2 protein in dividing tissues.

The next two papers investigate the control of lateral root formation. Firstly researchers from Glasgow look at how potassium signaling integrates with both the mechanisms of RNA-directed DNA-methylation and the auxin response. The other paper looks at how auxin signaling integrates with the plasmodesmata development and includes co-authors from the University of Nottingham.

The eighth paper is led from Nottingham and looks at the role of the PROTEOLYSIS (PRT)1 during the plant immune response whilst the next paper, which is from the University of Cambridge, also looks at plant immunity, specifically at how the biosynthesis of phytic acid impacts this response.

The remaining four papers include UK-based co-authors from University of South Wales, Rothamsted and Cardiff, Durham, Oxford and Aberystwyth in international research teams led from Malaysian (the expression of Acyl-CoA-binding proteins in oil palm), China (the effect of silver nanoparticles on plant growth), Japan (convergent evolution of lateral organ formation) and Chile (the factors that influence grain filling in wheat) respectively.


Parker MT, Knop K, Sherwood AV, Schurch NJ, Mackinnon K, Gould PD, Hall AJ, Barton GJ, Simpson GG (2020) Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m(6)A modification. Elife. doi: 10.7554/eLife.49658 Open Access

Matt Parker, Kasia Knop, Anya Sherwood and Nicholas Schurch are co-first authors on this study from the University of Dundee at the James Hutton Institute in which they perform direct RNA sequencing using a nanopore sequencer. They used this technical advance to analyse the mRNA (m6A) methylome and reveal a contribution to the control of the circadian clock. Future use of this technique will undoubtedly allow for an improved annotation of the Arabidopsis genome (and others).

https://elifesciences.org/articles/49658

Dantas LLB, Calixto CPG, Dourado MM, Carneiro MS, Brown JWS, Hotta CT (2019) Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane. Front Plant Sci. doi: 10.3389/fpls.2019.01614 Open Access

This study is led from Brazil with Luiza Dantas as first author and includes co-authors from the University of Dundee at the James Hutton Institute. They investigate the level of alternative splicing (AS) in commercial sugarcane, which is an important C4 crop. Tissue samples were collected in winter and summer and this analysis reveals temperature- and organ-dependent differences in the levels of AS across a set of genes under circadian control.


Kostaki KI, Coupel-Ledru A, Bonnell VC, Gustavsson M, Sun P, Mclaughlin FJ, Fraser DP, McLachlan DH, Hetherington AM, Dodd AN, Franklin KA (2020). Guard cells integrate light and temperature signals to control stomatal aperture. Plant Physiol. doi: 10.1104/pp.19.01528 Open Access

Kalliopi-Ioanna Kostaki is first author on this study from the University of Bristol that begins to unpick the mechanisms that integrate light and temperature signals in the control of stomatal development. These signals converge on phototropin photoreceptors and multiple members of the 14-3-3 protein family. This work also reveals a currently uncharacterised pathway that controls temperature regulation of guard cell movement.


Zoulias N, Brown J, Rowe J, Casson SA (2020) HY5 is not integral to light mediated stomatal development in Arabidopsis. PLoS One. doi: 10.1371/journal.pone.0222480 Open Access

Nick Zoulias is first author on this study from the Casson lab at University of Sheffield. ELONGATED HYPOCOTYL 5 (HY5) is a key regulator of light-mediated development yet in this study the authors show that the HY5-signaling cascade does not play a role in stomatal development. This key finding shows that phytochrome and cryptochrome signaling in guard cells is transmitted via non-HY5 signaling components.


Galindo-Trigo S, Grand TM, Voigt CA, Smith LM (2020) A malectin domain kinesin functions in pollen and seed development in Arabidopsis. J Exp Bot doi: 10.1093/jxb/eraa023
This research from the Smith lab at the University of Sheffield is led by Sergio Galindo-Trigo. They show that MALECTIN DOMAIN KINESIN 2 (MDKIN2) is involved in pollen, embryo and endosperm development. Malectin domains bind polysaccharides and peptides when found extracellularly in receptor-like kinases so this might suggest that in dividing tissues MDKIN2 plays a role during the physical division of cells.


Shahzad Z, Eaglesfield R, Carr C, Amtmann A (2020) Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed. Nat Commun. doi: 10.1038/s41467-019-13927-3 Open Access

Zaigham Shahzad at the University of Glasgow is the first author in this study that looks at the relationship between potassium deficiency and lateral root formation. This effect is mediated via the impact of CLSY1, a key component of the RNA-directed DNA-methylation machinery, on the transcriptional repression of the AuxIAA protein IAA27. Interestingly this system appears to act as a backup to the auxin-dependent proteolysis pathway that is primarily responsible for the control of IAA27 activity.


Sager R, Wang X, Hill K, Yoo BC, Caplan J, Nedo A, Tran T, Bennett MJ, Lee JY (2019) Auxin-dependent control of a plasmodesmal regulator creates a negative feedback loop modulating lateral root emergence. Nat Commun. doi: 10.1038/s41467-019-14226-7.

This US study is led by Ross Sager and includes co-authors from the University of Nottingham. This research links the role of auxin in lateral root formation with plasmodesmata development through control of the plasmodesmal regulator PDLP5. They present a model wherein molecules required for lateral root emergence transit through plasmodesmata following an inductive auxin signal.


Till CJ, Vicente J, Zhang H, Oszvald M, Deery MJ, Pastor V, Lilley KS, Ray RV, Theodoulou FL, Holdsworth MJ (2019) The Arabidopsis thaliana N-recognin E3 ligase PROTEOLYSIS1 influences the immune response. Plant Direct. doi: 10.1002/pld3.194 Open Access

Christopher Till, Jorge Vicente and Hongtao Zhangis are co-first authors on this research led from the University of Nottingham and Rothamsted Research that involves use of quantitative proteomics to define the role of the N-recognin E3 ligase PROTEOLYSIS (PRT)1 during the plant immune response.


Poon JSY, Le Fevre RE, Carr JP, Hanke DE, Murphy AM (2019) Inositol hexakisphosphate biosynthesis underpins PAMP-triggered immunity to Pseudomonas syringae pv. tomato in Arabidopsis thaliana but is dispensable for establishment of systemic acquired resistance. Mol Plant Pathol. doi: 10.1111/mpp.12902
This research from the University of Cambridge is led by Jacquelyne Poon and Alex Murphy and looks at the role of the phytic acid (inositol hexakisphosphate, InsP6) biosynthesis in dividing tissues during the plant immune response. They characterize Arabidopsis plants with mutations in biosynthetic enzymes to show that there are multiple mechanisms of basal resistance that are dependent upon InsP6.


Amiruddin N, Chan PL, Azizi N, Morris PE, Chan KL, Ong PW, Rosli R, Masura SS, Murphy DJ, Sambanthamurthi R, Haslam RP, Chye ML, Harwood JL, Low EL (2019) Characterisation of Oil Palm Acyl-CoA-Binding Proteins and Correlation of their Gene Expression with Oil Synthesis. Plant Cell Physiol. doi: 10.1093/pcp/pcz237.
Nadzirah Amiruddin is lead author on this Malaysian-led research that includes collaborators from the University of South Wales, Rothamsted Research and Cardiff University. This paper looks at the expression of Acyl-CoA-binding proteins (ACBPs) in oil palm; providing important information about the role of this protein family during oil synthesis in the world’s most important oil crop.


Wang L, Sun J, Lin L, Fu Y, Alenius H, Lindsey K, Chen C (2019) Silver nanoparticles regulate Arabidopsis root growth by concentration-dependent modification of reactive oxygen species accumulation and cell division. Ecotoxicol Environ Saf. doi: 10.1016/j.ecoenv.2019.110072.

This Chinese-study is led by Likai Wang and includes Keith Lindsey from Durham University as a co-author. They look at the effect of silver nanoparticles (AgNPs) on growth of Arabidopsis. AgNPs are taken up by roots and have opposing effects at either 50 mg L-1 or 100mg mg L-1. This is an important preliminary study to understand how plant growth might be altered if AgNP’s are used as a delivery mechanism.


Naramoto S, Jones VAS, Trozzi N, Sato M, Toyooka K, Shimamura M, Ishida S, Nishitani K, Ishizaki K, Nishihama R, Kohchi T, Dolan L, Kyozuka J (2019) A conserved regulatory mechanism mediates the convergent evolution of plant shoot lateral organs. PLoS Biol. 2019 doi: 10.1371/journal.pbio.3000560 Open Access

This Japanese study is led by Satoshi Naramoto and Junko Kyozuka and includes co-authors from the University of Oxford. They performed a mutant screen in the liverwort Marchantia polymorpha to identify the LATERAL ORGAN SUPRESSOR 1 (MpLOS1) gene, which regulates meristem maintenance and lateral organ development. Remarkably they showed this gene is also functions in the control of lateral organ development in rice, therefore demonstrating convergent evolution across plant lineages in the control of lateral organs.


Del Pozo A, Méndez-Espinoza AM, Romero-Bravo S, Garriga M, Estrada F, Alcaíno M, Camargo-Rodriguez AV, Corke FMK, Doonan JH, Lobos GA (2020) Genotypic variations in leaf and whole-plant water use efficiencies are closely related in bread wheat genotypes under well-watered and water-limited conditions during grain filling. Sci Rep. doi: 10.1038/s41598-019-57116-0 Open Access

Alejandro del Pozo leads this Chilean study that includes co-authors from Aberystwyth and NIAB. This large-scale glasshouse experiment looked at the effect of water deficit on the growth of 14 bread wheat genotypes. Measurement of multiple parameters revealed that plants face limitations to the assimilation process during grain filling due to natural senesce and water stress.

GARNet Research Roundup: December 23rd 2019

The final GARNet Research Roundup of 2019 begins with three studies from the John Innes Centre. Firstly Steve Penfield’s group conducts a field-experiment that monitors FLC levels in winter oilseed rape. Second is a study from the Zilberman lab looking at the relationship between Histone H1 and DNA methylation.

Third is work from the Yant lab in JIC/Nottingham that investigates adaptive gene flow between Arabidopsis arenosa and Arabidopsis lyrata.

The next two papers are led from the Etchells lab in Durham, the first has developed a vascular-localised transcriptional network and the second is a methods paper for image analysis.

The sixth paper includes co-authors from Southampton and investigates nuclear-chloroplast signaling in Arabidopsis mediated by the GUN1 protein.

The next two papers include members of the current GARNet advisory committee. Yoselin Benitez-Alfonso from the University of Leeds is an author on a paper that models plasmodesma geometry whilst members of the Kaiserli lab in Glasgow are involved in a study that investigates the factors involved in auxin-dependent thermomorphogenesis.

The Dupree lab in Cambridge leads the next research paper that looks at the detailed composition of the cell wall in the softwood Spruce.

The next two papers are from the Sainsbury lab, Norwich. Firstly the Kamoun lab looks at the molecular code of a plant NLR immune receptors whilst in the second paper members of the Zipfel lab are co-authors on a study that looks at defence-related protease activity from a fungal pathogen of strawberry.

The twelfth paper is from Ian Graham’s lab at the University of York and looks at the role of light signaling during seed development.

Sue Armstrong from Birmingham is a co-author on the next paper in which researchers present a genetic map of the field cress Lepidium campestre.

The final two papers include researchers from Royal Holloway University of London and look at the role of different transcription factors during embryo or root meristem development.


O’Neill CM, Lu X, Calderwood A, Tudor EH, Robinson P, Wells R, Morris R, Penfield S (2019) Vernalization and Floral Transition in Autumn Drive Winter Annual Life History in Oilseed Rape. Curr Biol. doi: 10.1016/j.cub.2019.10.051
Open Access

Carmel O’Neill is first author on the research from the Morris and Penfield labs at the John Innes Centre. This paper describes experiments that monitored FLC levels in field-growth winter oilseed rape. Surprisingly they shows that decline of FLC during October in relatively mild-temperatures of 10-15C reduce FLC levels, leading to floral transition prior to the colder winter temperatures. This work shows the importance of field experiments to understand real-world mechanisms that control crop development.


Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D (2019) DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. Mol Cell. doi: 10.1016/j.molcel.2019.10.011
This research from the Zilberman lab at the John Innes Centre is led by Jaemyoung Choi and looks at the relationship between histone H1 and the DNA methylation machinery during the maintenance of transcriptional homeostasis.

https://www.sciencedirect.com/science/article/abs/pii/S1097276519307890?via%3Dihub

Marburger S, Monnahan P, Seear PJ, Martin SH, Koch J, Paajanen P, Bohutínská M, Higgins JD, Schmickl R, Yant L (2019) Interspecific introgression mediates adaptation to whole genome duplication. Nat Commun. doi: 10.1038/s41467-019-13159-5
Open Access

Sarah Marburger from Levi Yant’s lab at the John Innes Centre/University of Nottingham leads this research that includes co-authors from Leicester, Edinburgh and the Czech Republic. They look at the effect of whole-genome duplication on gene flow between Arabidopsis arenosa and Arabidopsis lyrata.


Smit M, McGregor S, Sun H, Gough C, Bågman AM, Soyars CL, Kroon JTM, Gaudinier A, Williams CJ, Yang X, Nimchuk ZL, Weijers D, Turner SR, Brady SM, Etchells P (2019) A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis. Plant Cell. doi: 10.1105/tpc.19.00562
Open Access

This large-scale systems-biology paper is a UK-US-China-Dutch collaboration led by Margot Smit at Wageningen, Shauni McGregor and Peter Etchells at Durham University. They have developed a detailed transcriptional network based on the vascular-localised PHLOEM INTERCALATED WITH XYLEM (PXY) receptor kinase.

http://www.plantcell.org/content/early/2019/12/05/tpc.19.00562.long

Bagdassarian KS, Connor KA, Jermyn IH, Etchells JP (2019) Versatile method for quantifying and analyzing morphological differences in experimentally obtained images. Plant Signal Behav. doi: 10.1080/15592324.2019.1693092
This paper from Peter Etchells lab in Durham is led by Kristine Bagdassarian and introduces a bespoke method for inspecting the differences between the morphologies of several plant mutants at the cellular level.


Shimizu T, Kacprzak SM, Mochizuki N, Nagatani A, Watanabe S, Shimada T, Tanaka K, Hayashi Y, Arai M, Leister D, Okamoto H, Terry MJ, Masuda T (2019) The retrograde signaling protein GUN1 regulates tetrapyrrole biosynthesis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1911251116

Open Access

Sylwia M. Kacprzak and Matthew Terry from the University of Southampton are co-authors on this Japanese-led study that looks at the interaction between nuclear and chloroplast genomes as controlled by role that the GUN1 protein plays in control of tetrapyrrole metabolism.

https://www.sciencedirect.com/science/article/abs/pii/S1097276519307890?via%3Dihub

Deinum EE, Mulder BM, Benitez-Alfonso Y (2019) From plasmodesma geometry to effective symplasmic permeability through biophysical modelling. Elife. doi: 10.7554/eLife.49000
Open Access

Eva Deinum is lead author of this study that includes GARNet Committee member Yoselin Benitez-Alfonso as co-author. They have applied biophysical modeling to calculate effective symplasmic permeability for the transport of molecules through plasmodesmata. The resulting open-source model has been refined through experimental observations.

Dr Deinum will be leading a GARNet-supported workshop on this multilevel model during the July 2020 EMBO workshop on ‘Intercellular communication and plasmodesmata in plant development and disease’.


van der Woude LC, Perrella G, Snoek BL, van Hoogdalem M, Novák O, van Verk MC, van Kooten HN, Zorn LE, Tonckens R, Dongus JA, Praat M, Stouten EA, Proveniers MCG, Vellutini E, Patitaki E, Shapulatov U, Kohlen W, Balasubramanian S, Ljung K, van der Krol AR, Smeekens S, Kaiserli E, van Zanten M (2019) HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1911694116

This wide collaboration is led by Lennard van der Woude at Utrecht University and includes Giorgio Perrella and Eirini Kaiserli from Glasgow as co-authors. This research looks at the complex relationship between thermomorphogenesis, auxin and light signaling, histone deacylation and the regulation of histone variant H2A.Z.


Terrett OM, Lyczakowski JJ, Yu L, Iuga D, Franks WT, Brown SP, Dupree R, Dupree P (2019) Molecular architecture of softwood revealed by solid-state NMR. Nat Commun. doi: 10.1038/s41467-019-12979-9

Open Access

This research from the Dupree lab in Cambridge is led by Olivier Terrett and uses solid-state NMR to analyse the cell wall composition of the softwood spruce, in part through comparison with Arabidopsis cell walls. This information is an essential requirement to build experimental strategies for the biorefining of particular wood-types.


Adachi H, Contreras M, Harant A, Wu CH, Derevnina L, Sakai T, Duggan C, Moratto E, Bozkurt TO, Maqbool A, Win J, Kamoun S (2019) An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species. Elife. doi: 10.7554/eLife.49956

Open Access

Hiroaki Adachi leads this study from lab of Sophien Kamoun at the Sainsbury lab, Norwich. In this research they interrogate the molecular code of a plant NLR immune receptor to identify the minimal functional motifs that are required to induce hypersensitive cell death in response to a plant pathogen.

https://elifesciences.org/articles/49956

Caro MDP, Holton N, Conti G, Venturuzzi AL, Martínez-Zamora MG, Zipfel C, Asurmendi S, Díaz-Ricci JC (2019) The fungal subtilase AsES elicits a PTI-like defence response in Arabidopsis thaliana plants independently of its enzymatic activity. Mol Plant Pathol. doi: 10.1111/mpp.12881
Open Access

Nicolas Holton and Cyril Zipfel from the Sainsbury Lab in Norwich are co-authors on this Argentinian-led study with María del Pilar Caro as both first and corresponding author. They characterize the proteolytic role of the elicitor subtilisin (AsES) from strawberry fungal pathogen Acremonium strictum during an immune response.


Barros-Galvão T, Dave A, Gilday AD, Harvey D, Vaistij FE, Graham IA (2019) ABA INSENSITIVE4 promotes rather than represses PHYA-dependent seed germination in Arabidopsis thaliana. New Phytol. doi: 10.1111/nph.16363
Open Access

Thiago Barros-Galvão and Ian Graham at the University of Leeds lead this research that investigates the role of phytochrome A (PHYA) and PHYB signaling during seed development in Arabidopsis.

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16363

Desta ZA, Kolano B, Shamim Z, Armstrong SJ, Rewers M, Sliwinska E, Kushwaha SK, Parkin IAP, Ortiz R, de Koning DJ (2019) Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes. Sci Rep. doi: 10.1038/s41598-019-53320-0

Open Access

This Swedish led study has Zeratsion Abera Desta as lead author and includes Sue Armstrong from the University of Birmingham as a co-author. They have produced an early genome map of field cress (Lepidium campestre), which is a potential oilseed plant. They show that diploid Lepidium campestre has 16 chromosomes.


Leviczky T, Molnár E, Papdi C, Őszi E, Horváth GV, Vizler C, Nagy V, Pauk J, Bögre L, Magyar Z (2019) E2FA and E2FB transcription factors coordinate cell proliferation with seed maturation. Development. doi: 10.1242/dev.179333
Open Access

Tünde Leviczky is first author on this Hungarian-led study that includes co-authors from Royal Hollaway University of London. This work characterises the role of the E2F transcription factors and the RETINOBLASTOMA-RELATED repressor protein during Arabidopsis embryo development.

https://dev.biologists.org/content/146/22/dev179333.long

Lokdarshi A, Papdi C, Pettko-Szandtner A, Dorokhov S, Scheres B, Magyar Z, von Arnim AG, Bogre L, Horváth B (2019) ErbB-3 BINDING PROTEIN 1 Regulates Translation and Counteracts RETINOBLASTOMA RELATED to Maintain the Root Meristem. Plant Physiol. doi: 10.1104/pp.19.0080
This UK-US-Hungary collaboration includes Ansul Lokdarshi and Csaba Papdi as co-first authors and Laszlo Bogre and Beatrix Horvath from Royal Hollaway University of London as corresponding authors. They assessed the role of the ErbB-3 BINDING PROTEIN 1 transcription factor during Arabidopsis root meristem development

GARNet Research Roundup: November 22nd 2019

This bumper edition of the GARNet Research Roundup begins with three papers that have a focus on the circadian clock. First is from Cambridge and looks at a novel role for TTG1 in control of the clock. The second paper also includes co-authors from Cambridge and looks at the clock Evening Complex. The final clock paper includes co-authors from York and looks at the new roles for EARLY FLOWERING 3 and GIGANTEA.

The next four papers include researchers from the John Innes Centre. Yiling Ding’s lab lead an exciting study into the role of RNA G-quadruplex to define liquid-liquid phase separations. Next David Seung and Alison Baker look at production of amylose starch across Arabidopsis accessions. The third JIC paper is from the Charpentier lab and looks at nuclear calcium signaling in the root. Finally Lars Ostergaard is a co-author on a paper that identifies a novel biostimulant that controls podshatter in Brassica.

The eighth paper is from Glasgow and describes the bioengineering of plants to express a novel antibiotic bacteriocin.

Next are three papers introduce exciting new research tools. 1. Weibei Yang in the Meyerowitz lab introduces a method for co-labeling of RNAs and protein 2. Researchers in Nottingham introduce RootNav2.0 for the automated measurement of root archtiectures 3. The Haydon Lab has developed a GAL4-GFP luciferase system for tissue-specific gene expression analysis.

Two Photosynthesis-based papers come next with firstly an analysis on the link between metabolism and the light response curve (from Manchester) and secondly a look at the role of aquaporins in control of CO2 conductance (Cambridge and Lancaster).

The fourteenth paper is from Durham and characterises an important protein regulator of the autophagy-dependent degradation pathway whilst the fifteenth is from Cambridge and uses cryo-SEM to analyse cell wall structures.

The penultimate paper is from Birmingham and looks at the role of redox signaling in aphid fecundity and the final paper includes co-authors from RHUL and looks at the interaction between the E2FB and RETINOBLASTOMA-RELATED proteins.


Airoldi CA, Hearn TJ, Brockington SF, Webb AAR, Glover BJ (2019) TTG1 proteins regulate circadian activity as well as epidermal cell fate and pigmentation. Nat Plants. doi: 10.1038/s41477-019-0544-3

This study from the University of Cambridge is led by Chiara Airoldi and introduces a new role for the TRANSPARENT TESTA GLABRA 1 (TTG1) WD-repeat (WDR) subfamily in the regulation of the circadian clock. TTG1 regulates epidermal cell differentiation and pigment production, while LIGHT-REGULATED WD1 and LIGHT-REGULATED WD2A are known to regulate the clock. The triple lwd1 lwd2 ttg1 mutant has no detectable circadian rhythym. This suggests that members of this protein family have undergone subfunctionalization to diverge from their core functions. This paper is of interest to those who research evolution of protein function as well as the to those interested in the control of the circadian clock.

https://www.nature.com/articles/s41477-019-0544-3

Tong M, Lee K, Ezer D, Cortijo S, Jung J, Charoensawan V, Box MS, Jaeger K, Takahashi N, Mas P, Wigge PA, Seo PJ (2019) The Evening Complex establishes repressive chromatin domains via H2A.Z deposition. Plant Physiol. doi: 10.1104/pp.19.00881

This collaboration between the UK and South Korea is led by Meixuezi Tong and investigates how the Evening Complex (EC) component of the circadian clock interacts with chromatin to control gene expression at dusk. This occurs through direct interaction with the SWI2/SNF2-RELATED complex and together they bind to the core clock genes PRR7 and PRR9, causing the deposition of H2A.Z at these loci subsequent to causing their repression at dusk.


Anwer MU, Davis A, Davis SJ, Quint M (2019) Photoperiod sensing of the circadian clock is controlled by EARLY FLOWERING 3 and GIGANTEA. Plant J. doi: 10.1111/tpj.14604

Amanda Davies and Seth Davies from the University of York are co-authors on this German-led study with Muhammad Anwer as both first and corresponding author. They look at the role of important circadian regulators ELF3 and GIGANTEA through generation of previously unanalysed elf3gi double mutants. In these plants the circadian oscillator fails to synchronize to light-dark cycles even under diurnal conditions, demonstrating that these genes act together to convey photoperiod sensing to the central oscillator.


Zhang Y, Yang M, Duncan S, Yang X, Abdelhamid MAS, Huang L, Zhang H, Benfey PN, Waller ZAE, Ding Y (2019) G-quadruplex structures trigger RNA phase separation. Nucleic Acids Res. doi: 10.1093/nar/gkz978
Open Access

Yueying Zhang is the first author of this study conducted in the lab of Yiliang Ding at the John Innes Centre, in collaboration with the Benfey lab in the USA. They reveal an exciting mode of regulating RNA activity through the formation of RNA G-quadruplex (GQ) complexes. They use the SHORTROOT mRNA as the model for this study, showing that GQ-mediated complex formation can bring liquid-liquid phase separation. This study is of fundamental importance as it provides the first evidence that RNA can adopt structural motifs to trigger and/or maintain the specificity of RNA-driven phase separation.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz978/5624975?guestAccessKey=d3913912-fdbb-4f35-aa71-625442722842

Seung D, Echevarría-Poza A, Steuernagel B, Smith AM (2019) Natural polymorphisms in Arabidopsis result in wide variation or loss of the amylose component of starch. Plant Physiol. doi: 10.1104/pp.19.01062
Open Access

David Seung at the John Innes Centre the first and corresponding author of this study that used data from the Arabidopsis 1135 Genome project to investigate the prevelance of amylose production. Plants with amylose-free starch have no detrimental phenotypes so the function of this glucose-polymer, that accounts for up to 30% of all natural starch, is unknown. They looked at the polymorphisms within the GRANULE-BOUND STARCH SYNTHASE (GBSS) enzyme, identifying natural accessions that have no GBSS activity yet are viable within their natural environments. This study is a prelude to future research that will discover the adaptive significance of amylose.


Leitão N, Dangeville P, Carter R, Charpentier M (2019) Nuclear calcium signatures are associated with root development. Nat Commun. doi: 10.1038/s41467-019-12845-8
Open Access

Nuno Leitao is first author on this research from the Charpentier lab at the John Innes Centre. They looked at the role of nuclear Ca2+ signalling on primary root meristem development and auxin homeostasis through activity of the nuclear membrane localised ion channel DOES NOT MAKE INFECTIONS 1 (DMI1). This study discovers a previously unappreciated role for intracellular Ca2+ signalling during plant development.


Łangowski Ł, Goñi O, Quille P, Stephenson P, Carmody N, Feeney E, Barton D, Østergaard L, O’Connell S (2019 A plant biostimulant from the seaweed Ascophyllum nodosum (Sealicit) reduces podshatter and yield loss in oilseed rape through modulation of IND expression. Sci Rep. doi: 10.1038/s41598-019-52958-0
Open Access

Lars Ostergaard is a co-author on this Irish-study led by Lukasz Łangowski that investigates the factors that control pod shatter in oil seed rape. They show that the seaweed Ascophyllum nodosum-based biostimulant (Sealicit) is able to reduce podshatter by effecting the expression of the major regulator of pod shattering, INDEHISCENT. This has implications for the use of this compound by farmers wanting to reduce the amount of seed loss due to premature pod shatter.


Rooney WM, Grinter RW, Correia A, Parkhill J, Walker DC, Milner JJ (2019) Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae. Plant Biotechnol J. doi: 10.1111/pbi.13294
Open Access

William Rooney at the University of Glasgow is lead author on this study that attempts to combat Pseudomonas syringae infections through expression of a novel protein antibiotic bacteriocin, putidacin. They show that transgenic expression of this bacterial protein provides effective protection against Pseudomonas. This proof of concept opens the possibility for more widespread use of bacteriocins as an effective plant protection strategy.

https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.13294

Yang W, Schuster C, Prunet N, Dong Q, Landrein B, Wightman R, Meyerowitz EM (2019) Visualization of Protein Coding, Long Non-coding and Nuclear RNAs by FISH in Sections of Shoot Apical Meristems and Developing Flowers. Plant Physiol. doi: 10.1104/pp.19.00980
This extended methods paper is led by Weibing Yang at the Sainsbury lab in Cambridge. They have adapted RNA fluorescence in situ hybridization (rnaFISH) to explore RNA localization in the shoot apical meristem of Arabidopsis. They are able to label mRNA as well as long ncRNAs and have developed double labeling to assay two separate RNAs in the same cell and to assess nucleo-cytoplasmic separation of RNA species. Finally they link rnaFISH with fluorescence immunocytochemistry for the simultaneous localization of a single genes mRNA and protein.

https://www.frontiersin.org/articles/10.3389/fpls.2019.01398/full

Yasrab R, Atkinson JA, Wells DM, French AP, Pridmore TP, Pound MP (2019) RootNav 2.0: Deep learning for automatic navigation of complex plant root architectures. Gigascience. doi: 10.1093/gigascience/giz123
Open Access

Robail Yasrab is lead author on this work from the University of Nottingham that introduces the RootNav2.0 software tool. This was developed by modern deep-learning approaches and allows the fully automated measurement of vertically growth root systems. RootNav2.0 was favourably compared with its semi-automated predecessor RootNav1.0 and can be used for measurement of root architectures from a range of different plant species.


Román Á, Golz JF, Webb AA, Graham IA, Haydon MJ (2019) Combining GAL4 GFP enhancer trap with split luciferase to measure spatiotemporal promoter activity in Arabidopsis. Plant J. doi: 10.1111/tpj.14603

This technical advance is led by Angela Roman, was in the Haydon lab during its time at the University of York. They have used the GAL4-GFP enhancer trap system, to develop a tissue-specific split luciferase assay for non-invasive detection of spatiotemporal gene expression in Arabidopsis. In this example they use the study to measure dynamics of circadian gene expression but is clearly applicable to answer many other experimental questions.


Herrmann HA, Schwartz JM, Johnson GN (2019) From empirical to theoretical models of light response curves – linking photosynthetic and metabolic acclimation. Photosynth Res. doi: 10.1007/s11120-019-00681-2
Open Access

Helena Herrmann is lead author on this work fro the University of Manchester. In this study they developed and then empirically tested a series of simple kinetic models that explains the metabolic changes that are required to alter light response curves (LRCs) across a range of temperatures. This allowed them to show how changes in NADPH and CO2 utilization respond to environmental changes. This provides useful information as to how a plant adapts its metabolic response to light depending on the growth temperature.

Helena explaining her research

Kromdijk J, Głowacka K, Long SP (2019) Photosynthetic efficiency and mesophyll conductance are unaffected in Arabidopsis thaliana aquaporin knock-out lines. J Exp Bot. doi: 10.1093/jxb/erz442

Open Access
Wanne Kromdijk leads this US-led research that includes contributions from the Universities of Cambridge and Lancaster. They looked at the potential role of membrane-bound aquaporins in the control of diffusion conductance for CO2 transfer from substomatal cavity to chloroplast stroma (gm). They tested three aquaporin mutants across a range of light and CO2 concentrations and surprisingly found that they appear to play no significant contribution to the control of gm. The reporting of this type of ‘negative’ result will prevent unnecessary replication of experiments and help to streamline the research process.


Wang P, Pleskot R, Zang J, Winkler J, Wang J, Yperman K, Zhang T, Wang K, Gong J, Guan Y, Richardson C, Duckney P, Vandorpe M, Mylle E, Fiserova J, Van Damme D, Hussey PJ (2019) Plant AtEH/Pan1 proteins drive autophagosome formation at ER-PM contact sites with actin and endocytic machinery. Nat Commun. doi: 10.1038/s41467-019-12782-6
Open Access

Pengwei Wang is first author in this research led from Durham University that incudes Chinese and Belgian collaborators. They show that the AtEH/Pan1 protein is involved with actin cytoskeleton regulated autophagy and recruits multiple other components to autophagosomes during this process. In addition they show vesicle bound-AtEH/Pan1 interact with VAP27-1 at the ER-PM. This demonstrates that AtEH/Pan1 is a key component of the autophagy-dependent degradation pathway.


Lyczakowski JJ, Bourdon M, Terrett OM, Helariutta Y, Wightman R, Dupree P (2019) Structural Imaging of Native Cryo-Preserved Secondary Cell Walls Reveals the Presence of Macrofibrils and Their Formation Requires Normal Cellulose, Lignin and Xylan Biosynthesis. Front Plant Sci. doi: 10.3389/fpls.2019.01398
Open Access

Jan Lyczakowski from the Dupree lab at the University of Cambridge is first author on this study that has adapted low temperature scanning electron microscopy (cryo-SEM) to visualize the cell walls of both angiosperm and gymnosperms. They have used Arabidopsis mutants to reveal that cell wall macrofibrils at composed of cellulose, xylan, and lignin. They demonstrate that cryo-SEM is a useful tool for native nanoscale cell wall architectures.


Rasool B, Karpinska B, Pascual J, Kangasjärvi S, Foyer CH (2019) Catalase, glutathione and protein phosphatase 2A-dependent organellar redox signalling regulate aphid fecundity under moderate and high irradiance. Plant Cell Environ. doi: 10.1111/pce.13669
Brwa Rasool is first author on this collaboration between the Universities of Birmingham and Helsinki that looks at how aphids respond to redox changes in Arabidopsis thaliana grown under different light conditions. They also identified defence-related transcription factors differentially upregulated by aphid predation in different light conditions. Overall they show aphid fecundity is in part determined by the plants cellular redox signaling.


Őszi E, Papdi C, Mohammed B, Pettkó-Szandtner A, Vaskó-Leviczky T, Molnár E, Ampudia CG, Khan S, Lopez-Juez E, Horváth B, Bögre L, Magyar Z (2019) E2FB interacts with RETINOBLASTOMA RELATED and regulates cell proliferation during leaf development. Plant Physiol. doi: 10.1104/pp.19.00212
Erika Oszi is first author of this Hungarian-led research that includes co-authors from Royal Holloway University of London. This research looks at the interaction between the transcription factors E2FB and RETINOBLASTOMA-RELATED (RBR) and how this contributes to cell proliferation during organ development in Arabidopsis leaves. The relationship between these proteins changes throughout the stages of leaf development and is critical to determine final leaf cell number.

http://www.plantphysiol.org/content/early/2019/11/06/pp.19.00212.long

GARNet Research Roundup: October 17th 2019

This edition of the GARNet Research Roundup includes a superb selection of papers by scientists from across the UK. First is work from the Spoel lab in Edinburgh that characterizes the fine-tuning of NPR1 activity during the plant immune response. Second is work from SLCU and the University of Helsinki that is an extensive investigation into the molecular basis of cambial development. Next is research from Nottingham that looks at the importance of soil macro-structures during the growth of wheat roots.

Fourth are three papers that highlight the breadth of research occurring at the John Innes Centre. The first paper is from Enrico Coen’s lab that applies their expertise in computational modeling to leaf development in the carnivorous plant Utricularia gibba. Second is work from Saskia Hogenhout’s lab that looks at immunity to infection by Phytoplasma pathogens. Last is work from Lars Ostergaard’s lab that characterises the role of Auxin Binding promoter elements in floral development.

The seventh paper from Bristol and Glasgow looks at shade avoidance signaling via PIF5, COP1 and UVR8 whilst the eighth paper, which is from Rothamsted, demonstrates how metabolic engineering in Arabidopsis seeds can result in a high proportion of human milk fat substitute. The next paper is from the University of Durham and investigates how the composition of the Arabidopsis cell wall impacts freezing tolerance. The first author of this paper, Dr Paige Panter discusses the paper on the GARNet community podcast.

The tenth paper is from Julia Davies’s lab at the University of Cambridge and introduces an uncharacterised response to extracellular ATP signals in Arabidopsis roots. The next paper is from Mike Blatt’s group at University of Glasgow and characterises a new interaction between vesicular transport and ion channels. The penultimate entry includes co-authors from the JIC on a Chinese-led study that demonstrates improved seed vigour in wheat through overexpression of a NAC transcription factor. Finally are two methods papers taken from a special journal issue on ‘Plant Meiosis’.


Skelly MJ, Furniss JJ, Grey HL, Wong KW, Spoel SH (2019) Dynamic ubiquitination determines transcriptional activity of the plant immune coactivator NPR1. Elife. doi: 10.7554/eLife.47005
Open Access

Michael Skelly is lead author on this paper from the lab of current GARNet chair Steven Spoel. In it they investigate the mechanisms that fine-tune the function of NPR1, a key player in the plant immune response. Progressive ubiquitination of NPR1 by an E3 ligase causes both its interaction with target genes and its subsequent degradation by an E4 ligase. This latter occurrence is opposed by the deubiquitinase activity of UBP6/7, setting up a complex regulatory environment that allows the plant to rapidly response to pathogen attack.


Zhang J, Eswaran G, Alonso-Serra J, Kucukoglu M, Xiang J, Yang W, Elo A, Nieminen K, Damén T, Joung JG, Yun JY, Lee JH, Ragni L, Barbier de Reuille P, Ahnert SE, Lee JY, Mähönen AP, Helariutta Y (2019) Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots. Nat Plants. doi: 10.1038/s41477-019-0522-9

This pan-European-Korean collaboration has Jing Zhang from the University of Helsinki and the Sainsbury Laboratory, University of Cambridge as first author. They use cambium cell-specific transcript profiling and follow-on network analysis to discover 62 new transcription factors involved in cambial development in Arabidopsis. This information was used to engineer plants with increased radial growth through ectopic cambial activity as well as to generate plants with no cambial activity. This understanding provides a platform for possible future improvements in production of woody biomass.


Atkinson JA, Hawkesford MJ, Whalley WR, Zhou H, Mooney SJ (2019) Soil strength influences wheat root interactions with soil macropores. Plant Cell Environ. doi: 10.1111/pce.13659
This work is led from the University of Nottingham by John Atkinson and Sacha Mooney. They use X-ray Computed Tomography to investigate a trait called trematotropism, which applies to the ability of deep rooting plants to search out macropores and avoid densely packed soil. They show root colonisation of macropores is an important adaptive trait and that strategies should be put in place to increase these structures within the natural soil environment.


Lee KJI, Bushell C, Koide Y, Fozard JA, Piao C, Yu M, Newman J, Whitewoods C, Avondo J, Kennaway R, Marée AFM, Cui M, Coen E (2019) Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism. PLoS Biol. doi: 10.1371/journal.pbio.3000427
Open Access

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000427

Karen Lee, Claire Bushell and Yohei Koide are co-first authors on this work led by Enrico Coen at the John Innes Centre and Minlong Cui at the Zhejiang Agriculture and Forestry University in China. This study uses 3D imaging, cellular and clonal analysis, combined with computational modelling to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. They identify growth ansiotrophies that result in the final leave shape that develops from an initial near-spherical form. These processes have some similarities to the polar growth seen in Arabidopsis leaves. Overall they show that ‘simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies’.


Pecher P, Moro G, Canale MC, Capdevielle S, Singh A, MacLean A, Sugio A, Kuo CH, Lopes JRS, Hogenhout SA (2019) Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize. PLoS Pathog. doi: 10.1371/journal.ppat.1008035
Open Access

This work from Saskia Hogenhout’s lab at the John Innes Centre is led by Pascal Pecher and Gabriele Moro. They look at the effect of SAP11 effectors from Phytoplasma species that infect either Arabidopsis or maize. They demonstrate that although both related versions of SAP11 destabilise plant TCP transcription factors, their modes of action have significant differences. Please look out for Saskia discussing this paper on the GARNet Community podcast next week.


Kuhn A, Runciman B, Tasker-Brown W, Østergaard L 92019) Two Auxin Response Elements Fine-Tune PINOID Expression During Gynoecium Development in Arabidopsis thaliana. Biomolecules. doi: 10.3390/biom9100526
Open Access

Andre Kuhn is first author of this research from Lars Østergaard’s lab at the John Innes Centre. They functional characterise two Auxin-responsive Elements (AuxRE) within the promotor of the PINOID gene, which are bound by the ETITIN/ARF3 Auxin Response Factor. Alteration of this AuxRE causes phenotypic changes during flower development demonstrating that even with a complex regulatory environment, small changes to cis-elements can have significant developmental consequences.


Sharma A, Sharma B, Hayes S, Kerner K, Hoecker U, Jenkins GI, Franklin KA (2019) UVR8 disrupts stabilisation of PIF5 by COP1 to inhibit plant stem elongation in sunlight. Nat Commun. doi: 10.1038/s41467-019-12369-1
Open Access

Ashutosh Sharma is first author of this UK-Spanish-Germany collaboration led by Keara Franklin at University of Bristol. They have characterised the interaction between three significant molecular players that function during the shade avoidance response in Arabidopsis; PIF5, UVR8 and COP1. In shaded conditions, UVR8 indirectly promotes rapid degradation of PIF5 through their interactions with the E3 ubiquitin ligase COP1.


van Erp H, Bryant FM, Martin-Moreno J, Michaelson LV, Bhutada G, Eastmond PJ (2019) Engineering the stereoisomeric structure of seed oil to mimic human milk fat. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1907915116

Open Access

Harrie Van Arp and Peter Eastmond at Rothamsted Research lead this extremely translational study in which they have modified the metabolic pathway for triacylglycerol (TAG) biosynthesis. By modifying the location of one biosynthesis enzyme and removing the activity of another, the fats produced in these Arabidopsis seeds are enriched to contain TAGs that are similar to those found in human milk. They propose that this technology could be used to develop a source of plant-derived human milk fat substitute.


Panter PE, Kent O, Dale M, Smith SJ, Skipsey M, Thorlby G, Cummins I, Ramsay N, Begum RA, Sanhueza D, Fry SC, Knight MR, Knight H (2019) MUR1-mediated cell-wall fucosylation is required for freezing tolerance in Arabidopsis thaliana. New Phytol. doi: 10.1111/nph.16209

Paige Panter led this work as part of her PhD at the University of Durham in the lab of Heather Knight. They characterise the role of the MUR1 protein in the control of cell wall fucosylation and how this contributes to plant freezing tolerance. Paige discusses this paper and the long history of MUR1 on the GARNet Community podcast. Please check it out!


Wang L, Stacey G, Leblanc-Fournier N, Legué V, Moulia B, Davies JM (2019) Early Extracellular ATP Signaling in Arabidopsis Root Epidermis: A Multi-Conductance Process. Front Plant Sci. doi: 10.3389/fpls.2019.01064.

Open Access

The UK-French collaboration is led by Limin Wang from Julia Davies’s lab in Cambridge. They use patch clamp electrophysiology to identify previously uncharacterized channel conductances that respond to extracellular ATP across the root elongation zone epidermal plasma membrane.


Waghmare S, Lefoulon C, Zhang B, Lileikyte E, Donald NA, Blatt MR (2019) K+ channel-SEC11 binding exchange regulates SNARE assembly for secretory traffic. Plant Physiol. doi: 10.1104/pp.19.00919

Open Access

This work from Mike Blatt’s lab in Glasgow is led by Sakharam Waghmare. They look at the interaction between SNARE proteins, which are involved in vesicular fusion and K+ channels, which help control turgor pressure during cell expansion. Through combining analysis of protein-protein interactions and electrophysiological measurement they have found that this interaction requires the activity of the regulatory protein SEC11.


Li W, He X, Chen Y, Jing Y, Shen C, Yang J, Teng W, Zhao X, Hu W, Hu M, Li H, Miller AJ, Tong Y (2019) A wheat transcription factor positively sets seed vigour by regulating the grain nitrate signal. New Phytol. doi: 10.1111/nph.16234
Wenjing Li is first author of this Chinese study that includes Yi Chen and Anthony Miller from the John Innes Centre as co-authors. This research shows that seed vigour and nitrate accumulation in wheat is regulated by the TaNAC2 transcriptions factor through its control of the TaNRT2.5 nitrate transporter. The authors suggest that both genes could be used as potential future targets to increase grain yield and nitrogen use efficiency.


The Special Issue of Methods in Molecular Biology on Plant Meiosis includes papers from the University of Cambridge, led by Christophe Lambing and the James Hutton Institute, led by Benoit Darrier.

Lambing C, Choi K, Blackwell AR, Henderson IR (2019) Chromatin Immunoprecipitation of Meiotically Expressed Proteins from Arabidopsis thaliana Flowers. Methods Mol Biol. doi: 10.1007/978-1-4939-9818-0_16
Darrier B, Arrieta M, Mittmann SU, Sourdille P, Ramsay L, Waugh R, Colas I (2019) Following the Formation of Synaptonemal Complex Formation in Wheat and Barley by High-Resolution Microscopy. Methods Mol Biol. doi: 10.1007/978-1-4939-9818-0_15

GARNet Research Roundup: June 12th 2019

In another big edition of the GARNet Research Roundup we cover many different areas of research that utilise a varied group of experimental organisms!

The first paper from the Feng lab at the John Innes Centre performs an assessment of the factors influencing heterochromatin activity in sperm companion cells. Second is work from the JIC and Cardiff University that looks at the role of an auxin minima during fruit valve margin differentiation.

The next two papers have authors from Edinburgh. Firstly the McCormick lab has developed a stereo-based 3D imaging system for plants while Steven Spoel is a co-author on a study that looks at the pathogen responsive gene NPR1.

Coming from across the M8 is a paper from the Christie lab in Glasgow that looks into using phototropin genes as potential targets for crop improvement.

The next paper is from Oxford Brookes University where they visualise the movement of protein nanodomain clusters within the plasma membrane. Elsewhere in Oxford is a paper from the van der Hoorn group that characterises the effect of a novel triazine herbicide.

Two papers from the University of Durham also identify and characterise the role of novel herbicides, in this case on the activity of inositol phosphorylceramide synthases.

The final five papers feature research that each use different experimental organisms. Firstly a paper from the Earlham Institute uses delayed fluorescence to investigate the circadian clock in wheat and OSR. Second is a paper from Warwick that assesses the role of nodulation during nitrogen uptake in Medicago. The next paper features the Yant lab at University of Nottingham looks at growth of two species of Arabidopsis in challenging environments.

The penultimate paper includes authors from the University of Oxford and provides a detailed analysis of the factors controlling leaf shape in Cardamine and Arabidopsis thaliana. The final paper uses the imaging facility at the Hounsfield facility in Nottingham to image the roots of date palms.


He S, Vickers M, Zhang J, Feng X (2019) Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. Elife. doi: 10.7554/eLife.42530

Open Access

Lead author on his paper is Shengbo He from Xiaoqi Feng’s lab at the John Innes Centre. This work looks at activation of Transposable elements (TEs) in the sperm companion cell of Arabidopsis. This is catalyzed by the DEMETER-catalyzed DNA demethylation in regions depleted of histone H1, demonstrating a key role for H1 in determining heterochromatin activity.

https://elifesciences.org/articles/42530

Li XR, Vroomans RMA, Fox S, Grieneisen VA, Østergaard L, Marée AFM (2019) Systems Biology Approach Pinpoints Minimum Requirements for Auxin Distribution during Fruit Opening. Mol Plant. doi: 10.1016/j.molp.2019.05.003

Open Access

Xin-Ran Li and Renske Vroomans are co-lead authors on this work from the Ostergaard, Grieneisen and Maree labs from the John Innes Centre and (now) Cardiff University.They look at the role of an auxin minima in the control of valve margin differentiation in Arabidopsis fruit. They used a cycle of experimental-modeling to develop a model that predicts the maturation of the auxin minimum to ensure timely fruit opening and seed dispersal.


Bernotas G, Scorza LCT, Hansen MF, Hales IJ, Halliday KJ, Smith LN, Smith ML, McCormick AJ (2019) A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth. Gigascience. doi: 10.1093/gigascience/giz056

Open Access

Gytis Bernotas from UWE and Livia Scorza from the McCormick lab at the University of Edinburgh lead this work that is the result of a 2+ year collaboration with the Melvyn Smith and others at the Computer Machine Vision (CMV) facility at UWE. The authors have developed hardware and software (including a deep neural network) to automate the 3D imaging and segmentation of rosettes and individual leaves using a photometric stereo approach.

https://academic.oup.com/gigascience/article/8/5/giz056/5498634

Chen J, Mohan R, Zhang Y, Li M, Chen H, Palmer IA, Chang M, Qi G, Spoel SH, Mengiste T, Wang D, Liu F, Fu ZQ (2019) NPR1 promotes its own and target gene expression in plant defense by recruiting CDK8. Plant Physiol. doi: 10.1104/pp.19.00124

GARNet chairman Steven Spoel is a co-author on this US-led study with Jian Chen as lead author. The paper investigates the interacting partners of NPR1 (NONEXPRESSER OF PR GENES 1), which is a master regulator of salicyclic signaling and therefore an important regulation of plant defense response.


Hart JE, Sullivan S, Hermanowicz P, Petersen J, Diaz-Ramos LA, Hoey DJ, Łabuz J, Christie JM (2019) Engineering the phototropin photocycle improves photoreceptor performance and plant biomass production. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1902915116

Open Access

Jaynee Hart is first author on this research from Christie lab at the University of Glasgow in which they target the phototropin blue light receptor as a candidate for crop improvement. They showed plants that engineered to have a slow-photocycling version of PHOT1 or PHOT2 had increased biomass under low light conditions, due to their increased sensitivity to low light.


McKenna JF, Rolfe DJ, Webb SED, Tolmie AF, Botchway SW, Martin-Fernandez ML, Hawes C, Runions J (2019) The cell wall regulates dynamics and size of plasma-membrane nanodomains in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1819077116

Open Access

Joe McKenna from Oxford Brookes University leads this work that takes advantage of their superb imaging facilities to assess the dynamic regulation of specific protein clusters in the Arabidopsis plasma membrane. They show that the cytoskeleton (both actin and microtubule) and the cell wall play roles in the control of intra-PM moment of the pathogen receptor FLS2 and the auxin transporter PIN3.

https://www.pnas.org/content/early/2019/06/07/1819077116

Morimoto K, Cole KS, Kourelis J, Witt CH, Brown D, Krahn D, Stegmann M, Kaschani F, Kaiser M, Burton J, Mohammed S, Yamaguchi-Shinozaki K, Weerapana E, van der Hoorn RAL (2019) Triazine probes targeting ascorbate peroxidases in plants. Plant Physiol. doi: 10.1104/pp.19.00481

Open Access

Kyoko Morimoto is first author on this UK-German-Japanese collaboration led from the lab of GARNet committee member Renier van der Hoorn. They characterise the herbicidal effect of the small 1,3,5-triazine KSC-3 on ascorbate peroxidases (APXs) across a range of plant species.


Pinneh EC, Stoppel R, Knight H, Knight MR, Steel PG, Denny PW (2019) Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana. PLoS One. doi: 10.1371/journal.pone.0217087

Open Access

Pinneh EC, Mina JG, Stark MJR, Lindell SD, Luemmen P, Knight MR, Steel PG, Denny PW (2019) The identification of small molecule inhibitors of the plant inositol phosphorylceramide synthase which demonstrate herbicidal activity. Sci Rep. doi: 10.1038/s41598-019-44544-1

Open Access

Elizabeth Pinneh leads these two papers from the Denny lab in Durham. In the first paper they use RNAseq data and analysis of overexpression transgenic lines to define the role of inositol phosphorylceramide synthase (IPCS) during abiotic and biotic stress responses.

Secondly they screened a panel of 11000 compounds for their activity against the AtIPCS2 in a yeast two-hybrid assay. Successful hits from the screen were confirmed with in vitro enzyme assays and in planta against Arabidopsis.


Rees H, Duncan S, Gould P, Wells R, Greenwood M, Brabbs T, Hall A (2019) A high-throughput delayed fluorescence method reveals underlying differences in the control of circadian rhythms in Triticum aestivum and Brassica napus. Plant Methods. doi: 10.1186/s13007-019-0436-6

Open Access

Hannah Rees from Anthony Hall’s lab at the Earlham Institute leads this methods paper that introduces the use of delayed fluorescence to investigate the circadian rhythms in wheat and oil seed rape.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0436-6

Lagunas B, Achom M, Bonyadi-Pour R, Pardal AJ, Richmond BL, Sergaki C, Vázquez S, Schäfer P, Ott S, Hammond J, Gifford ML (2019) Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula. Mol Plant. doi: 10.1016/j.molp.2019.03.014

Open Access

Beatriz Lagunas is lead author on this paper from the University of Warwick that investigates the role of nodulation in actual nitrogen uptake by the roots of Medicago truncatula. They use integrated molecular and phenotypic analysis to determine that the respond to nitrogen flux are processed on a whole plant level through multiple developmental processes.

https://www.cell.com/molecular-plant/fulltext/S1674-2052(19)30127-3?

Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L (2019) Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils Philos Trans R Soc Lond B Biol Sci. doi: 10.1098/rstb.2018.0243

Open Access

Veronica Preite is first author on this UK-German collaboration led by Ute Kraemer and Levi Yant in Nottingham. They performed whole genome resequenced of 64 individuals of two Arabidopsis species that grow on calamine metalliferous sites (which have toxic levels of the zinc and cadmium). They revealed a modest amount of gene and network convergence in plants that have colonised these challenging environments.


Kierzkowski D, Runions A, Vuolo F, Strauss S, Lymbouridou R, Routier-Kierzkowska AL, Wilson-Sánchez D, Jenke H, Galinha C, Mosca G, Zhang Z, Canales C, Dello Ioio R, Huijser P, Smith RS, Tsiantis M (2019) A Growth-Based Framework for Leaf Shape Development and Diversity. doi: 10.1016/j.cell.2019.05.011

Open Access

Claudia Canales and Carla Galinha from Oxford are co-authors on this German-led study from Miltos Tsiantis’ lab that performs a detailed dissection of the growth parameters that control differences in leaf-shape in Cardamine and Arabidopsis. They show critical roles for the SHOOTMERISTEMLESS and REDUCED COMPLEXITY homeobox proteins to define differences in shape determination.


Xiao T, Raygoza AA, Pérez JC, Kirschner G, Deng Y, Atkinson B, Sturrock C, Lube V, Wang JY, Lubineau G, Al-Babili S, Ramírez LAC, Bennett MJ, Blilou I (2019) Emergent Protective Organogenesis in Date Palms: A Morpho-devo-dynamic Adaptive Strategy During Early Development. Plant Cell. doi: 10.1105/tpc.19.00008

Open Access

Members of the Hounsfield CT Imaging Facility 
at the University of Nottingham are co-authors on this paper that is led by Tingting Xiao from KAUST in Saudi Arabia. The paper takes a detailed look at root morphology in Date Palm.

GARNet Research Roundup: May 27th 2019

This bumper edition of the GARNet research roundup begins with a set of papers from the John Innes Centre. Anne Osbourn’s group is involved with two papers; firstly they discover how altering metabolic networks in the Arabidopsis root can cause changes in the associated microbiota. Second they characterise the role of a light-induced transcription factor in Artemisia. Next Caroline Dean’s group leads a global consortium that investigates the role of liquid-liquid phase separation in the formation of nuclear bodies. The final paper from the JIC is from Philippa Borrill and Cristobal Uauy, in which they identify novel transcription factors in wheat.

The fourth paper is led by Peter Etchells at Durham and characterises receptor kinase activity involved in vascular patterning in Arabidopsis.

The next two papers focus on stomatal patterning; firstly Julie Gray’s group at Sheffield looks at the stomatal responses to long-term pathogen infections. The second paper is from Glasgow and describes improvements in the OnGuard2 software, which models the factors controlling stomatal density.

Jose Gutierrez-Marcos is a co-author on a paper that uses FACS/ATAC-seq to define chromatin changes within cells of the shoot apical meristem. Richard Harrison leads the next paper that is also method-focused; describing use of CRISPR-Cas9 gene editing in Strawberry.

Andrew Miller at the University of Edinburgh is the corresponding author of the penultimate paper, which presents a whole-life-cycle, multi-model Framework that links many aspects of the Arabidopsis life cycle. The final paper is Seth Davies’s group at York and investigates the role of sucrose in the control of the circadian clock.


Huang AC, Jiang T, Liu YX, Bai YC, Reed J, Qu B, Goossens A, Nützmann HW, Bai Y, Osbourn A (2019) A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science. doi: 10.1126/science.aau6389

Ancheng Huang and Ting Jiang are first authors on this UK, Chinese and Belgian collaboration led by Anne Osbourn at the John Innes Centre. They reconstitute three biosynthesic pathways in the Arabidopsis roots and show how this affects the associated microbiota.


Hao X, Zhong Y, Nützmann HW, Fu X, Yan T, Shen Q, Chen M, Ma Y, Zhao J, Osbourn A, Li L, Tang K (2019) Light-induced artemisinin biosynthesis is regulated by the bZIP transcription factor AaHY5 in Artemisia annua. Plant Cell Physiol. doi: 10.1093/pcp/pcz084

Anne Osbourn is a co-author on this Chinese-led study that has identified that the basic leucine zipper transcription factor (TF) AaHY5 regulated of light-induced biosynthesis of artemisinin in Artemisia annua.


Fang X, Wang L, Ishikawa R, Li Y, Fiedler M, Liu F, Calder G, Rowan B, Weigel D, Li P, Dean C (2019) Arabidopsis FLL2 promotes liquid-liquid phase separation of polyadenylation complexes. Nature. doi: 10.1038/s41586-019-1165-8

Xiaofeng Fang, Liang Wang and Ryo Ishikawa are first authors of this UK, German and Chinese collaboration led by Caroline Dean’s lab at the John Innes Centre. They characterise the molecular factors that are required for the formation of nuclear bodies through liquid-liquid phase separation (PDF). These proteins are the Arabidopsis RNA-binding protein FCA and the coiled-coil protein FLL2.

From https://www.nature.com/articles/s41586-019-1165-8

Borrill P, Harrington SA, Simmonds J, Uauy C (2019) Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling. Plant Physiol. doi: 10.1104/pp.19.00380

Open Access

Philippa Borrill, now a faculty member at the University of Birmingham, conducted this work with Cristobal Uauy at the John Innes Centre. They have developed a range of research tools for use in wheat and this paper describes the identification of novel transcription factors involved in senescence.


Wang N, Bagdassarian KS, Doherty RE, Kroon JT, Connor KA, Wang XY, Wang W, Jermyn IH, Turner SR, Etchells JP (2019) Organ-specific genetic interactions between paralogues of the PXY and ER receptor kinases enforce radial patterning in Arabidopsis vascular tissue. Development. doi: 10.1242/dev.177105

Ning Wang works with Peter Etchells at Durham University where they have characterised the interactions between the receptor kinase gene families that regulate radial patterning in the development of vascular tissue.


Dutton C, Hõrak H, Hepworth C, Mitchell A, Ton J, Hunt L, Gray JE (2019) Bacterial infection systemically suppresses stomatal density. Plant Cell Environ. doi: 10.1111/pce.13570

Christian Dutton leads this work conducted at the University of Sheffield. They have investigated the longer-term systemic response to the presence of pathogens that involves reducing stomatal density. This process is mediated via salicylic acid signaling and slows disease progression.

From https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.13570

Jezek M, Hills A, Blatt MR, Lew VL (2019) A constraint-relaxation-recovery mechanism for stomatal dynamics. Plant Cell Environ. doi: 10.1111/pce.13568

Mareike Jezek leads this work from the University of Glasgow in which they have updated the OnGuard2 modelling software that has demonstrated substantial predictive power to describe stomatal dynamics. Their improvements allow for the development of models that are more similar to in vivo observations.


Frerichs A, Engelhorn J, Altmüller J, Gutierrez-Marcos J, Werr W (2019) Specific chromatin changes mark lateral organ founder cells in the Arabidopsis thaliana inflorescence meristem. J Exp Bot. doi: 10.1093/jxb/erz181

Jose Gutierrez-Marcos from the University of Warwick is a co-author on this German study led by Anneke Frerichs in which they analysed the chromatin state of lateral organ founder cells (LOFCs) in the peripheral zone of the Arabidopsis inflorescence meristem in wildtype and apetala1-1 cauliflower-1 double mutants. Importantly they showed that the combined application of FACS/ATAC-seq is able to detect chromatin changes in a cell-type specific manner.


Wilson FM, Harrison K, Armitage AD, Simkin AJ, Harrison RJ (2019) CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in diploid and octoploid strawberry. Plant Methods. doi: 10.1186/s13007-019-0428-6. eCollection 2019

Open Access

This paper is lead by Fiona Wilson at NIAB-EMR in which they present their methods to undertake gene editing in the challenging experimental system of diploid and octoploid strawberries.

From https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0428-6

Zardilis A, Hume A, Millar AJ (2019) A multi-model framework for the Arabidopsis life cycle. J Exp Bot. doi: 10.1093/jxb/ery394

Open Access

Argyris Zardilis conducted this modeling-focussed research at University of Edinburgh. The authors present a whole-life-cycle, multi-model Framework that links vegetative, inflorescence as fruit growth as well as seed dormancy in Arabidopsis. This Framework allows the authors to simulate at the population level in various genotype × environment scenarios.

From https://academic.oup.com/jxb/article/70/9/2463/5336616

Philippou K, Ronald J, Sánchez-Villarreal A, Davis AM, Davis SJ (2019) Physiological and Genetic Dissection of Sucrose Inputs to the Arabidopsis thaliana Circadian System. Genes (Basel). doi: 10.3390/genes10050334

Open Access

Koumis Philippou from Seth Davis’ research group the University of York leads this work that investigates the role of sucrose into the function of the circadian clock.

GARNet Research Roundup: December 21st 2018

This bumper Festive Edition of the GARNet Research Roundup begins with two papers that have Beatriz Orosa-Puente as lead author following her work on SUMOylation with Ari Sadanandom at Durham. These papers looks at the role of SUMOylation in either auxin-mediated hydropatterning or in the defence response. Malcolm Bennett at Nottingham is a co-author on both papers and provided an audio description of the auxin-focused paper on the GARNet YouTube channel.

The next three papers are from the University of Edinburgh, the first that defines the role of HECT ubiquitin ligases in the defence response, the second that conducts a proteomic analysis of the GIGANTEA-interactome and the third that introduces a set of new tools for inducible gene expression in Arabidopsis roots.

The sixth and seventh papers feature authors from the John Innes Centre. Martin Howard and Caroline Dean are corresponding authors on a multi-scale analysis of the factors that control FLC expression whilst Myriam Charpentier’s lab has contributed to an investigation about LINC complexes in Medicago.

David Salt and Levi Yant from Nottingham lead the next paper that provides an analysis of the genetic determinants of adaptation to different salt conditions.

The final three papers are from Cambridge. Firstly Ian Henderson is the corresponding author on work that looks at crossover rates in specific disease resistance loci. Second is work from the Paszkowski lab at SLCU that introduces a new method for the analysis of active retrotransposons in crop plants whilst finally James Locke, also at SLCU, uses the method of distributed delays to simplify the complexity of biological network models.


Orosa-Puente B, Leftley N, von Wangenheim D, Banda J, Srivastava AK, Hill K, Truskina J, Bhosale R, Morris E, Srivastava M, Kümpers B, Goh T, Fukaki H, Vermeer J, Vernoux T, Dinneny JR, French AP, Bishopp A, Sadanandom A , Bennett MJ (2018) Roots branch towarss water by post-translational modification of the transcription factor ARF7 Science DOI: 10.1126/science.aau3956

Orosa B, Yates G, Verma V, Srivastava AK, Srivastava M, Campanaro A, De Vega D, Fernandes A, Zhang C, Lee J, Bennett MJ, Sadanandom A (2018) SUMO conjugation to the pattern recognition receptor FLS2 triggers intracellular signalling in plant innate immunity. Nat Commun. doi: 10.1038/s41467-018-07696-8 Open Access

http://science.sciencemag.org/content/362/6421/1407

Beatriz Orosa-Puente is the lead author on two publications that have arisen from a collaboration between the labs of Ari Sadanandom at Durham and Malcolm Bennett at Nottingham. In the first paper Beatriz is co-first author with Nicola Leftley and Daniel von Wangenheim in research that links the auxin response, SUMOylation and the search for water. They reveal a novel mechanism for controlling the auxin response in which SUMOylation regulates the interaction between the ARF7 and IAA3 proteins. In turn this controls asymmetric expression of genes downstream of ARF7 and determines how different parts of the root response to the presence or absence of water.

The second paper continues with the Sadanandom lab’s focus on SUMOylation, in this case during control of the defence response. They show that SUMO is conjugated to the FLAGELLIN-SENSITIVE 2 (FLS2) receptor that senses bacterial flagellin. This releases downstream cytoplasmic effectors and enhances the immune response. The authors show that there is additional complexity to this system by also showing that flagellin induces degradation of the deSUMOylating enzyme Desi3a, thus allowing the plant to make a stronger immune response.


Furniss JJ, Grey H, Wang Z, Nomoto M, Jackson L, Tada Y, Spoel SH (2018) Proteasome-associated HECT-type ubiquitin ligase activity is required for plant immunity. PLoS Pathog. doi: 10.1371/journal.ppat.1007447 Open Access

James Furniss is the lead author on this paper from the lab of current GARNet Chairman Steven Spoel at the University of Edinburgh. They show that a family of HECT domain-containing ubiquitin protein ligases (UPLs) are involved in defence responses mediated by the hormone salicylic acid (SA). Upl3 mutants show reprogramming of the entire SA transcriptional response and they are unable to establish immunity against a hemi-biotrophic pathogen, demonstrating their key role in this important process.


https://febs.onlinelibrary.wiley.com/doi/abs/10.1002/1873-3468.13311

Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, LeBihan T, Halliday KJ, Imaizumi T, Millar AJ (2018) Time-resolved Interaction Proteomics of the GIGANTEA Protein Under Diurnal Cycles in Arabidopsis. FEBS Lett. doi: 10.1002/1873-3468.13311 Open Access

This paper is a collaboration between researchers in Edinburgh and Seattle for which Johanna Krahmer is lead author. They used a proteomic approach to identify proteins that interacted with a tagged-version of the key circadian regulator GIGANTEA. They successfully identified the novel transcription factor CYCLING DOF FACTOR (CDF)6. CDF6 was confirmed as interacting with GI and playing a role in the control of flowering. The time series of proteomic data produced in this study is available for use by any other interested researcher.

http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD006859


Machin FQ, Beckers M, Tian X, Fairnie A, Cheng T, Scheible WR, Doerner P (2018) Inducible reporter/driver lines for the Arabidopsis root with intrinsic reporting of activity state. Plant Journal. doi: 10.1111/tpj.14192

Frank Qasim Machin is the lead author on this Technical Advance from Peter Doerner’s lab at the University of Edinburgh. They have developed a Gateway-based system for tightly controlled inducible expression across all the major cell types of the Arabidopsis roots. They have fully characterised reference driver lines that can be adapted for specific experimental requirements and hope that this contributes towards enhancing reproducibility of qualitative and quantitative analyses.


https://www.sciencedirect.com/science/article/pii/S2405471218304368?via%3Dihub

Antoniou-Kourounioti RL, Hepworth J, Heckmann A, Duncan S, Qüesta J, Rosa S, Säll T, Holm S, Dean C, Howard M (2018) Temperature Sensing Is Distributed throughout the Regulatory Network that Controls FLC Epigenetic Silencing in Vernalization. Cell Syst. doi: 10.1016/j.cels.2018.10.011 Open Access

This work results from the successful collaboration between Caroline Dean and Martin Howard at the John Innes Centre and includes Rea Antoniou-Kourounioti and Jo Hepworth as co-first authors. They attempt to understand how the upregulation of VERNALIZATION INSENSITIVE3 (VIN3) and silencing of FLOWERING LOCUS C (FLC) is controlled during fluctuating temperatures over month-long time scales. They develop a mathematical model that integrates information from hour, day and month-long datasets to show that temperature is sensed across the entire regulatory network and not focussed on specific nodes. This allows a final effect to only be realised once all parts of the network have been appropriately changed. This model with matches new field data and therefore represents a predictive tool for the effects of climate change on plant growth.


Newman-Griffis AH, Del Cerro P, Charpentier M, Meier I (2018) Medicago LINC complexes function in nuclear morphology, nuclear movement, and root nodule symbiosis Plant Physiol. http://www.plantphysiol.org/content/early/2018/12/10/pp.18.01111 Open Access
Pablo del Cerro and Myriam Charpentier at the John Innes Centre are co-authors on this paper from Iris Meier’s lab at The Ohio State University. They identify and characterise the Linker of Nucleoskeleton and Cytoskeleton (LINC) family of nucleus-membrane-associated proteins. They show that, as in Arabidopsis, these proteins are required for nucleus movement in the root tip cells of Medicago truncatula and that they are an important contributor to nodulation. Both Iris and Myriam are members of the INDEPTH consortium that includes researchers who study this broad area of plant cell biology.


https://www.pnas.org/content/early/2018/12/11/1816964115.long

Busoms S, Paajanen P, Marburger S, Bray S, Huang XY, Poschenrieder C, Yant L, Salt DE (2018) Fluctuating selection on migrant adaptive sodium transporter alleles in  coastal Arabidopsis thaliana. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1816964115 Open Access

This UK-Sino-Spanish collaboration is led by David Salt and Levi Yant at the University of Nottingham. Silvia Busoms is the first author on the study that investigates the genetics of adaptive salt tolerance in a cohort of 77 individuals grown across a salinity gradient in a coastal region of Catalonia. By integrating their data with the 1135 genomes project they are able to trace the ancestry of these populations and define that growth in high salt conditions is associated with increased expression of the high-affinity K+ transporter (HKT1;1). This demonstrates that this gene plays a key role in the adaptation to salt stress.


Serra H, Choi K, Zhao X, Blackwell AR, Kim J, Henderson IR. Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes (2018) PLoS Genet. doi: 10.1371/journal.pgen.1007843 Open Access

This UK-Korean collaboration is led by the Heidi Serra and Ian Henderson at the University of Cambridge. They mapped the meiotic crossover hotspots that are located within the RAC1 and RPP13 disease resistance genes in Arabidopsis. They assessed these locations in plants with altered recombination rates and surprisingly showed that these effects have little impact at the RAC1 loci. Therefore they show that chromosome location and local chromatin environment are important for regulation of crossover activity. Overall they demonstrate that interhomolog divergence is important in shaping recombination within plant disease resistance genes and crossover hotspots.


Cho J, Benoit M, Catoni M, Drost HG, Brestovitsky A, Oosterbeek M, Paszkowski J (2018) Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. Nat Plants. doi: 10.1038/s41477-018-0320-9

Open Access with link: rdcu.be/bdLjy

For the second edition in succession, the GARNet research roundup features work from Jerzy Paszkowski’s lab at SLCU. In this case Jungnam Cho is lead author on work that has developed a new technique called ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for analysis of transposon-rich genomes from crop plants. Through characterisation of extrachromosomal linear DNA (eclDNA), ALE-seq allows the identification of active transposons. The authors use this technique in both rice and tomato and successfully identify a set of developmentally regulated transposable elements. This paper includes details of a bioinformatic pipeline that is adapted for ALE-seq data analyses, the scripts for which are available on GitHub.


Tokuda IT, Akman OE, Locke JCW. Reducing the Complexity of Mathematical Models for the Plant Circadian Clock by Distributed Delays (2018) J Theor Biol. doi: 10.1016/j.jtbi.2018.12.014

This UK-Japanese study includes James Locke at SLCU as corresponding author. They address the challenge of integrating an increasing number of parameters into large biological network models. Their system of study is the Arabidopsis circadian clock and they use the method of distributed delays to simplify the complexity of existing models. They demonstrate this effect by updating a model that explains the regulation of the PRR9 and PRR7 genes by LHY. They use recent experimental data and revise the previous model to show that it is more accurately reproduces the LHY-induction experiments of core clock genes. As stated they show that overall use of distributed delays facilitates the optimisation and reformulation of genetic network models.

GARNet Research Roundup: November 22nd 2018

This GARNet Research Roundup begins with two studies from the University of Sheffield. First is research from Jurriaan Ton’s lab that looks at the interaction between CO2 concentration, the soil microbiome and plant growth. The second paper from Matt Davey and Peter Quick looks at the effect of cold acclimation on freezing tolerance in Arabidpsis lyrata.

The third study includes authors from Dundee and Durham and also looks at an impact of altered CO2 concentrations, in this case on nitrogen assimilation.

The next paper looks at the role of a GA signaling module on endosperm expansion during seed germination and includes authors from Nottingham and Birmingham.

The fifth paper includes Richard Morris at the JIC as a co-author and looks at the relationship between calcium signaling and changes in cellular pH. The penultimate study features co-authors from Warwick and Exeter in work that looks at the role of 3′-O-β-D-ribofuranosyladenosine during plant immunity. Finally is a paper that includes Steve Long from Lancaster and characterises the rubisco-chaperone BSD2.


Williams A, Pétriacq P, Beerling DJ, Cotton TEA, Ton J (2018) Impacts of Atmospheric CO(2) and Soil Nutritional Value on Plant Responses to Rhizosphere Colonization by Soil Bacteria. Front Plant Sci. doi: 10.3389/fpls.2018.01493

https://www.frontiersin.org/articles/10.3389/fpls.2018.01493/full

Open Access

Alex Williams is the lead author of this paper and works with Jurriaan Ton at the University of Sheffield. The impact of the soil rhizosphere on plant growth is emerging as an important growth determinant. In this paper the authors assess the role of altered [CO2] and soil carbon (C) and nitrogen (N) concentration in the colonisation of Arabidopsis roots by two different bacteria. Firstly they showed that altered [CO2] did not change the growth dynamics of the saprophytic bacteria Pseudomonas putida KT2440 and was independent of soil C or N. In contrast growth of the rhizobacterial strain Pseudomonas simiae WCS417 was sensitive to both changing [CO2] and soil composition. These results show the importance of the interaction between atmospheric CO2 and soil nutritional status during plant interactions with soil bacteria.


Davey MP, Palmer BG, Armitage E, Vergeer P, Kunin WE, Woodward FI, Quick WP (2018) Natural variation in tolerance to sub-zero temperatures among populations of Arabidopsis lyrata ssp. petraea. BMC Plant Biol. doi: 10.1186/s12870-018-1513-0

Open Access

Matthew Davey, now working in Cambridge, collaborated with Peter Quick at the University of Sheffield on this research that looks at the tolerance of Arabidopsis lyrata to freezing. They showed that populations from locations with colder winter climates were better able to survive subzero temperatures, particular when they have been acclimated at near zero for longer periods. This demonstrates that the adaptation of plants to cold temperatures allows them to better survive freezing, although surprisingly this effect is lessened when this acclimation period does not occur.


Andrews M, Condron LM, Kemp PD, Topping JF, Lindsey K, Hodge S, Raven JA (2018) Effects of elevated atmospheric [CO2] on nitrogen (N) assimilation and growth of C3 vascular plants will be similar regardless of N-form assimilated. J Exp Bot. doi: 10.1093/jxb/ery371

This UK-New Zealand collaboration is led by Mitchell Andrews and looks at the effect of elevated [CO2] on the nitrogen (N) assimilation when the plant is exposed to a variety of different N-sources. They show that in C3 plants the overall N assimilated will be the same whether the plant is under ammonium (NH4+) nutrition or under nitrate (NO3-) nutrition. These results are contrary to previous results that suggest elevated [CO2] reduces plant growth under NO3- nutrition.


Sánchez-Montesino R, Bouza-Morcillo L, Marquez J, Ghita M, Duran-Nebreda S, Gómez L, Holdsworth MJ, Bassel G, Oñate-Sánchez L (2018) A regulatory module controlling GA-mediated endosperm cell expansion is critical for seed germination in Arabidopsis. Mol Plant. doi: 10.1016/j.molp.2018.10.009 

https://www.sciencedirect.com/science/article/pii/S1674205218303356

Open Access

This Spanish-led project includes authors from the Universites of Nottingham and Birmingham. They look at the influence of a GA signalling module on endosperm cell separation, which is essential for Arabidopsis seed germination. They show the NAC transcription factors NAC25 and NAC1L control expression of the EXPANSION2 gene and that the GA signalling component RGL2 has a controlling influence by repressing this activity.


Behera S, Xu Z, Luoni L, Bonza C, Doccula FG, DeMichelis MI, Morris RJ, Schwarzländer M, Costa A (2018) Cellular Ca2+ signals generate defined pH signatures in plants. Plant Cell. doi: 10.1105/tpc.18.00655

Open Access

Richard Morris (John Innes Centre) is a co-author on this Italian-led study that investigates the role of Calcium ions in cell signalling. They use a set of genetically-encoded fluorescent sensors to visualise a link between Ca2+ signaling and changes in pH. If this link is maintained across all cell types it might represent an extra layer of complexity and control of cellular signal transduction.


Drenichev MS, Bennett M, Novikov RA, Mansfield J, Smirnoff N, Grant M, Mikhailov S (2018) A role for 3′-O-β-D-ribofuranosyladenosine in altering plant immunity. Phytochemistry. doi: 10.1016/j.phytochem.2018.10.016

https://www.sciencedirect.com/science/article/pii/S0031942218301997?via%3Dihub

This Russian-led study includes UK-based researchers Mark Bennett, Murray Grant, Nick Smirnoff and John Mansfield as co-authors. They show that the natural disaccharide nucleoside, 3′-O-β-D-ribofuranosyladenosine accumulated in plants infected with the bacterial pathogen P. syringae. Perhaps surprisingly the application of this nucleoside to the plant doesn’t effect bacterial multiplication, indicating that adds a significant metabolic burden to plants already battling new infections.


Conlan B, Birch R, Kelso C, Holland S, De Souza AP, Long SP, Beck JL, Whitney SM (2018) BSD2 is a Rubisco specific assembly chaperone, forms intermediary hetero-oligomeric complexes and is non-limiting to growth in tobacco. Plant Cell Environ. doi: 10.1111/pce.13473

Steve Long is a Professor at Lancaster Environment Centre and is a co-author on this Australia-led study that characterizes the role of the Rubisco chaperone BSD2 during Rubisco biogenesis. These results suggest this is the sole role of BSD2 and its activity is non-limiting to tobacco growth.

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