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