GARNet Research Roundup: April 29th 2019

This edition of the GARNet research roundup features fundamental plant science research conducted in a range of experimental organisms. Firstly Liam Dolan’s lab in Oxford looks at the function of bHLHs proteins in cell differentiation across land plant evolution. Secondly Anthony Hall’s group at the Earlham Institute have identified a novel RecQ helicase involved in work exclusively conducted in wheat. Thirdly researchers from Nottingham work with Arabidopsis to characterise an EXPANSIN protein essential for lateral root development.

The fourth paper is the first of two that look at germination and uses a new model, Aethionema arabicum, to study the role of light in seed dormancy. This work includes research from Royal Holloway. The second ‘dormancy’ paper is from Peter Eastmond’s lab at Rothamsted and further characterises the DOG1 gene in Arabidopsis. The penultimate paper includes co-authors from Warwick and Leeds and introduces a novel chemical inhibitor of auxin transport. The final paper from researchers in Birmingham introduces the 3DCellAtlas Meristem, a powerful tool for cellular annotation of the shoot apical meristem.


Bonnot C, Hetherington AJ, Champion C, Breuninger H, Kelly S, Dolan L (2019) Neofunctionalisation of basic helix loop helix proteins occurred when embryophytes colonised the land. New Phytol. doi: 10.1111/nph.15829 https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15829

Clemence Bonnot is lead author on this study from Liam Dolan’s lab at the University of Oxford in which the authors assess the role of ROOT HAIR DEFECTIVE SIX-LIKE (RSL) genes during evolution of plant development. They look at the function of a member of this bHLH transcription factor family called CbbHLHVIII identified in the charophyceaen alga Chara braunii. This gene is expressed at specific morphologically important regions in the algae and cannot rescue the function of related RSL genes in Marchantia or Arabidopsis. This suggests that the function of RSL proteins in cell differentiation has evolved by neofunctionalisation through land plant lineages.


Gardiner LJ, Wingen LU, Bailey P, Joynson R, Brabbs T, Wright J, Higgins JD, Hall N, Griffiths S, Clavijo BJ, Hall A (2019) Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol. 20(1):69. doi: 10.1186/s13059-019-1675-6 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1675-6

Open Access

Laura Gardiner and Anthony Hall lead this work that was conducted at the Earlham Institute and uses a bespoke set of bioinformatic tools that allow fundamental questions to be asked in hexaploid wheat. They looked at crossover and gene conversion frequencies in 13 recombinant inbred mapping populations and were able to identity an important QTL and confirm functionality for a novel RecQ helicase gene. This gene does not exist in Arabidopsis and therefore this discovery-motivated research needed to be conducted in wheat. They hope that this identification will provide future opportunities to tackle the challenge of linkage drag when attempting to develop new crops varieties.


Ramakrishna P, Ruiz Duarte P, Rance GA, Schubert M, Vordermaier V, Vu LD, Murphy E, Vilches Barro A, Swarup K, Moirangthem K, Jørgensen B, van de Cotte B, Goh T, Lin Z, Voβ U, Beeckman T, Bennett MJ, Gevaert K, Maizel A, De Smet I (2019) EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation. Proc Natl Acad Sci U S A. 2019 Apr 3. pii: 201820882. doi: 10.1073/pnas.1820882116 https://www.pnas.org/content/early/2019/04/02/1820882116.long

Open Access

This pan-European study is led by Priya Ramakrishna at the University of Nottingham and includes co-authors from the UK, Belgium, Germany and Denmark. The authors look at the lateral root development and characterise the function of the EXPANSIN A1 protein. This protein influences the physical changes in the cell wall that are needed to enable the asymmetry cell divisions that define the location of a new lateral root. Plants lacking EXPA1 function do not properly form lateral roots and are unable to correctly respond to an inductive auxin signal. This clearly demonstrates an important requirement for the activity of genes that transmit cell signals into the physical relationships that exist between cells.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0

Mérai Z, Graeber K, Wilhelmsson P, Ullrich KK, Arshad W, Grosche C, Tarkowská D, Turečková V, Strnad M, Rensing SA, Leubner-Metzger G, Scheid OM (2019) Aethionema arabicum: a novel model plant to study the light control of seed germination. J Exp Bot. pii: erz146. doi: 10.1093/jxb/erz146

https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz146/5428144

Open Access

This paper includes authors from the UK, Germany, Austria and the Czech Republic including Kai Graeber and Gerhard Leubner-Metzger at Royal Holloway. They introduce the Brassica Aethionema arabicum as a new model to investigate the mechanism of germination inhibition by light as they have identified accessions that are either light-sensitive or light-neutral. In contrast germination in Arabidopsis is stimulated by light. Transcriptome analysis of Aethionema arabicum accessions reveal expression changes in key hormone-regulated genes. Overall they show that largely the same module of molecular components are involved in control of of seed dormancy irrespective of the effect of light on germination. Therefore any phenotypic changes likely result from changes in the activity organisms-specific of these genes.

https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz146/5428144

Bryant FM, Hughes D, Hassani-Pak K, Eastmond PJ (2019) Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis. Plant Cell. pii: tpc.00892.2018. doi: 10.1105/tpc.18.00892 http://www.plantcell.org/content/early/2019/04/08/tpc.18.00892.long

Open Access

http://www.plantcell.org/content/early/2019/04/08/tpc.18.00892.long

Fiona Bryant is lead author on this research from Rothamsted Research that investigates the factors that control expression of the DOG1 gene, which is a key regulator of seed dormancy. They show that LEUCINE ZIPPER TRANSCRIPTION FACTOR67 (bZIP67) regulates DOG1 expression and have uncovered a mechanism that describes the temperature-dependent regulation of DOG1 expression. Finally they identity a molecular change that explains known allelic difference in DOG1 function, which informs different levels of dormancy in different accessions.


Oochi A, Hajny J, Fukui K, Nakao Y, Gallei M, Quareshy M, Takahashi K, Kinoshita T, Harborough SR, Kepinski S, Kasahara H, Napier RM, Friml J, Hayashi KI (2019) Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiol. 2019 Apr 1. pii: pp.00201.2019. doi: 10.1104/pp.19.00201 http://www.plantphysiol.org/content/early/2019/04/01/pp.19.00201.long

Open Access

http://www.plantphysiol.org/content/early/2019/04/01/pp.19.00201.long

This Japanese-led study includes co-authors from the Universities of Warwick and Leeds and describes the identification of a novel positive chemical modulator of auxin cellular efflux. This aptly named PInStatic Acid (PISA) prevents PIN protein internalization yet does not impact the SCFTIR1/AFB signaling cascade. Therefore the authors hope that PISA will be a useful tool for unpicking the cellular mechanisms that control auxin transport.


Montenegro-Johnson T, Strauss S, Jackson MDB, Walker L, Smith RS, Bassel GW. (2019) 3D Cell Atlas Meristem: a tool for the global cellular annotation of shoot apical meristems. Plant Methods. 15:33. doi: 10.1186/s13007-019-0413-0

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0

Open Access

Thomas Montenegro-Johnson, Soeren Strauss, Matthew Jackson and Liam Walker lead this methods paper that was prepared following research that took place at the University of Birmingham and the Max Planck Institute for Plant Breeding Research in Cologne. They describe the 3DCellAtlas Meristem, a tool allows the complete cellular annotation of cells within a shoot apical meristem (SAM), which they have successfully tested in both Arabidopsis and tomato. The authors state that ‘this provides a rapid and robust means to perform comprehensive cellular annotation of SAMs and digital single cell analyses, including cell geometry and gene expression’.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0


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