This edition of the GARNet research roundup has an initial focus on the shoot apical meristem. Firstly a study from the University of Birmingham performs network analysis to define the connections that control the global organisation of this tissue.
Second is the first of a group of papers involving authors from the Sainsbury Lab, Cambridge University and the University of Cambridge. Henrik Jönsson and Henrik Ahl contribute to a study that refines our understanding about the role of auxin in leaf dorsoventral patterning. Next from SLCU are two papers published in collaboration with the University of Helsinki that identify a set of novel regulators of cambial development.
The final SLCU paper from James Locke’s group attempts to tackle the challenging topic of ‘noise’ in biological systems. The final paper from the University of Cambridge investigate factors involved in karrikin signaling.
The penultimate paper characterises the LINC complex in monocots and includes authors from Oxford Brookes University whilst the final paper is from the University of York and performs a structural analysis of a key enzyme involved in the potential phytoremediation of TNT.
Jackson MDB, Duran-Nebreda S, Kierzkowski D, Strauss S, Xu H, Landrein B, Hamant O, Smith RS, Johnston IG, Bassel GW (2019) Global Topological Order Emerges through Local Mechanical Control of Cell Divisions in the Arabidopsis Shoot Apical Meristem. Cell Syst. doi: 10.1016/j.cels.2018.12.009
George Bassel is corresponding author of this paper led by Matthew Jackson
at the University of Birmingham. They use live 3D imaging and
computational analysis to identify a network of cellular connections in
the shoot apical meristem. They show that locally generated cell
division rules lead to emergence of global tissue organisation, which
facilitates cellular communication. In addition they show that global
cellular organization requires the activity of the KATANIN protein.
Bhatia N, Åhl H, Jönsson H, Heisler MG (2019) Quantitative analysis of auxin sensing in leaf primordia argues against proposed role in regulating leaf dorsoventrality. Elife. doi: 10.7554/eLife.39298
and Henrik Ahl at SLCU are co-authors on this study led by Neha Bhatia
at the University of Sydney. They use data gained from analysis of the
R2D2 auxin sensor to argue against the current hypothesis stating that
asymmetric auxin distribution is necessary to define the dorso-ventral
polarity of the Arabidopsis leaf. They repeat previous experiments using
the DII auxin sensor and through additional analysis using an auxin
insensitive version of the sensor (mDII), provide results that contrast
to previously published data.
Miyashima S, Roszak P, Sevilem I,
Toyokura K, Blob B, Heo JO, Mellor N, Help-Rinta-Rahko H, Otero S, Smet
W, Boekschoten M, Hooiveld G, Hashimoto K, Smetana O, Siligato R,
Wallner ES, Mähönen AP, Kondo Y, Melnyk CW, Greb T, Nakajima K, Sozzani
R, Bishopp A, De Rybel B, Helariutta Y (2019). Mobile PEAR transcription factors integrate positional cues to prime cambial growth. Nature doi: 10.1038/s41586-018-0839-y
O, Mäkilä R, Lyu M, Amiryousefi A, Sánchez Rodríguez F, Wu MF, Solé-Gil
A, Leal Gavarrón M, Siligato R, Miyashima S, Roszak P, Blomster T, Reed
JW, Broholm S, Mähönen AP (2019). High levels of auxin signalling define the stem-cell organizer of the vascular cambium. Nature. doi: 10.1038/s41586-018-0837-0
These back-to-back manuscripts include Pawel Roszak from the SLCU as an author in both papers. The corresponding author for the first paper, which is a true global collaboration, is Yrjo Helariutta who holds research positions at both SLCU and the University of Helsinki. These papers introduce a new signalling module of transcriptional factors that control radial growth initiated in procambial cells. In root protophloem cells cytokinin induces the expression of a newly characterised set of PEAR transcription factors, which form a short-range concentration gradient and initiate radial growth. To maintain tight developmental control of this program PEAR protein activity is antagonised by HD-ZIP III proteins, whose expression domain is controlled by the activity of auxin and a set of mobile miRNAs. The identification of this signalling module increases our understanding about the factors that control the growth of woody tissues and therefore has enormous translational significance.
Cortijo S, Aydin Z, Ahnert S, Locke JC (2019) Widespread inter-individual gene expression variability in Arabidopsis thaliana Mol Syst Biol. doi: 10.15252/msb.20188591
is the lead author of this paper and works with James Locke at SLCU.
They have attempted to address the fundamental question of noise within
biological outputs through analysis of gene expression from a set of
identical Arabidopsis plants grown in identical conditions. They
identify hundreds of genes that show variable expression between these
plants, with different gene sets changing throughout the diurnal cycle.
They further define this variability by identifying gene length, the
number of transcription factors regulating the genes and the chromatin
environment as contributory factors to explain why this variation
Swarbreck SM, Guerringue Y, Matthus E, Jamieson FJC, Davies JM (2019) Impairment in karrikin but not strigolactone sensing enhances root skewing in Arabidopsis thaliana. Plant J. doi: 10.1111/tpj.14233
is the first author of this work from Julia Davies’ lab at the
University of Cambridge. They show that perception of karrikins
(smoke-derived butenolides) through the interaction of the KAI2
hydrolase and MAX2 F-box protein occurs independent of
strigolactone-sensing mechanism of the MAX2-D14 hydrolase interaction.
Karrikins cause a root skewing phenotype so the authors use this output
to identify that previously characterised SMAX1 (SUPPRESSOR OF
MAX2-1)/SMXL2 and SMXL6,7,8 (SUPPRESSOR OF MAX2-1-LIKE) proteins are
targets of degradation by the KAI2/MAX2 complex. Overall they show that
KAI2/MAX2 limits root skewing but is not involved in the role KAI2 plays
in gravi- or mechano-sensing. These results are indicative of a set of
KAI2 specific ligands that control root skewing yet candidate proteins
for these roles remain to be identified.
Gumber HK, McKenna JF, Estrada AL, Tolmie AF, Graumann K, Bass HW (2019) Identification and characterization of genes encoding the nuclear envelope LINC complex in the monocot species Zea mays. J Cell Sci. doi: 10.1242/jcs.221390
paper is led by Hank Bass and Hardeep Gumber from Florida State
University and includes Joe McKenna, Andrea Tolmie and Katja Graumann at
Oxford Brookes as co-authors. They use phylogenetic and microscopic
analysis to identify and characterise components of the nuclear-envelope
spanning LINC (Linker of Nucleoskeleton to Cytoskeleton) complex in Zea mays.
They identify a set of monocot-specific members of the LINC complex,
which will allow an increased understanding about the functional
linkages between the cytoplasm, nuclear envelope, nucleoplasm and
Hank Bass discusses this paper on the GARNet YouTube channel. Hank and Katja are members of the EU COST action entitled ‘Impact of Nuclear Domains On Gene Expression and Plant Traits (INDEPTH).
Tzafestas K, Ahmad L, Dani MP, Grogan G, Rylott EL, Bruce NC (2018) Structure-Guided
Mechanisms Behind the Metabolism of 2,4,6-Trinitrotoluene by
Glutathione Transferases U25 and U24 That Lead to Alternate Product
Distribution Front Plant Sci. doi: 10.3389/fpls.2018.01846
is the first author on this paper from the University of York led by
Neil Bruce. They perform a structural analysis of the Arabidopsis tau
class glutathione transferase, GSTU25, which is involved in the
phytoremediation of 2,4,6-trinitrotoluene (TNT). This analysis
identified of a key set of amino acids involved in a precise part of its
enzymatic activity, which can in turn be transferred to the related,
but enzymatically-inert GSTU24. These findings will aid in the
development of increasingly efficient strategies for plant-based
remediation of environmental TNT.