GARNet Research Roundup: March 7th 2019

This edition of the GARNet research roundup begins with a study into the genetic basis of fertility in barley led by Sarah McKim from Dundee. Second is a study from Oxford and Leicester that characterizes the proteolytic control of chloroplast import. The third paper from Levi Yant’s group at JIC and Nottingham that attempts to discover the influence of polyploidism on population genomic effects whilst the fourth paper from Juliet Coates’ lab in Birmingham uses the growth of Arabidopsis to assess the potential of algal biomass as a biofertiliser. The next two papers include co-authors from Oxford and Warwick respectively and investigate different factors that control seed viability in Arabidopsis and Brassica oleracea. The final paper includes Seth Davies from York as a co-author on a study that looks at control of the circadian clock in field-grown Arabidopsis.


Zwirek M, Waugh R, McKim SM (2019) Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain. New Phytol. doi: 10.1111/nph.15548

Open Access

Current GARNet committee members Sarah McKim is the leader of this study in which first author is Monica Zwirek. They investigate the mechanism through which the barley VRS genes contribute to spikelet fertility. They undercover the epistatic relationship between five VRS genes that explains how they contribute to controlling fertility of lateral spikelets. Importantly they demonstrate that various vrs mutant combinations improve fertility in a variety of ways, information that will be useful during the generation of new varieties of barley.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15548

Ling Q, Broad W, Trösch R, Töpel M, Demiral Sert T, Lymperopoulos P, Baldwin A, Jarvis RP (2019) Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science. doi: 10.1126/science.aav4467

Qihua Ling and William Broad are the first authors on this study from the Universities of Oxford and Leicester. They investigate the role of proteolysis in the functional control of chloroplast-envelope translocases, which are required for the transport of proteins from nucleus-encoded genes into the chloroplast. They identify two newly characterised proteins that function in the same pathway as the known ubiquitin E3 ligase SP1. These novel proteins, SP2 and CDC48, are both required for the movement of ubiquitinated proteins from the chloroplast outer envelope membrane (OEM) into the cytosol, where they are degraded by the proteolytic machinery. This process of chloroplast-associated protein degradation (CHLORAD) maintains tight control of the activity of OEM proteins and is essential for organelle function.

http://science.sciencemag.org/content/363/6429/eaav4467.long

Monnahan P, Kolář F, Baduel P, Sailer C, Koch J, Horvath R, Laenen B, Schmickl R, Paajanen P, Šrámková G, Bohutínská M, Arnold B, Weisman CM, Marhold K, Slotte T, Bomblies K, Yant L (2019) Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nat Ecol Evol. doi: 10.1038/s41559-019-0807-4.

Patrick Monnahan at the John Innes Centre is first author on this study from the Yant lab that has recently moved to the University of Nottingham. In this collaboration with colleagues in the US, Austria, Sweden, the Czech Republic and Slovakia, they have performed large scale sequencing on 39 populations of Arabidopsis arenosa. These plants have differing levels of ploidy and they are attempting to understand how ploidy effects population genomics. They demonstrate that the ploidy effects are subtle but significant and that masking of deleterious mutations, faster substitution rates and interploidy introgression will likely impact the evolution of populations where polyploidy is common.


Ghaderiardakani F, Collas E, Damiano DK, Tagg K, Graham NS, Coates J (2019) Effects of green seaweed extract on Arabidopsis early development suggest roles for hormone signalling in plant responses to algal fertilisers. Sci Rep. doi: 10.1038/s41598-018-38093-2

Open Access

This work from the Coates lab at the University of Birmingham is led by Fatemeh Ghaderiardakani and looked into the potential of algal extracts as biofertiliser. They showed that at >0.1%, extracts taken from the common green seaweed Ulva intestinalis inhibit Arabidopsis seed germination and root elongation. At lower concentrations primary root elongation was promoted albeit with a complete loss of lateral root formation. Elemental analysis allows the authors to suggest that this effect was mediated via a novel mechanism involving aluminium. Overall the authors caution against the use of algal biofertilisers due to potential unforeseen negative effects on plant growth.


Viñegra de la Torre N, Kaschani F, Kaiser M, van der Hoorn RAL, Soppe WJJ, Misas Villamil JC (2019) Dynamic hydrolase labelling as a marker for seed quality in Arabidopsis seeds. Biochem J. doi: 10.1042/BCJ20180911.

GARNet Committee member Renier van der Hoorn is a co-author on this German-led study that investigates how the activity of seed-localised proteases can affect Arabidopsis seed germination. This study has clear real-world application regarding the storage of economically important seed stocks. They show that vacuolar processing enzymes (VPEs) become more active during aging whilst the activity of serine hydrolases declines alongside seed quality. This information has allowed the authors to develop protease-activity-based markers that will provide information about seed quality.


Schausberger C, Roach T, Stöggl WM, Arc E, Finch-Savage WE, Kranner I (2019) Abscisic acid-determined seed vigour differences do not influence redox regulation during ageing. Biochem J. doi: 10.1042/BCJ20180903

William Finch-Savage from the University of Warwick is a co-author on this Austrian-led study that looks at the effect of aging on the quality of Brassica oleracea seeds stored at two oxygen concentrations. Higher O2 causes a more rapid decrease in seed quality through aging yet in contrast aging did not alter the impact of the hormone ABA on seed viability. This study enables the authors to uncover two mechanisms that control seed quality that appear to act through different mechanisms.


Rubin MJ, Brock MT, Davis SJ, Weinig C (2019) QTL Underlying Circadian Clock Parameters Under Seasonally Variable Field Settings in Arabidopsis thaliana G3 (Bethesda). doi: 10.1534/g3.118.200770

Open Access

Seth Davies from the University of York is a co-author on this study led by Matthew Rubin from the University of Wyoming. They looked at the growth of Arabidopsis thaliana recombinant inbred lines grown in field conditions and found an extremely nuanced relationship regarding how QTLs that influence the circadian clock respond to environmental conditions. For example the authors showed that plant growth in June, July and September is controlled by different QTL architecture, demonstrating the complex regulation of the circadian clock in these field growth plants.

Arabidopsis Research Roundup: May 5th

There are a bumper crop of papers in this edition of the Arabidopsis Research Roundup. First from the University of Manchester is a paper that identifies a protein involved in plant programmed cell death. Secondly are two papers from the University of Bristol that highlight the role of viruses in the reflectivity of plant leaves and an assessment of the growth parameters of Arabidopsis on different soil-types. Thirdly are three papers from University of Edinburgh that either use CRISPR-Cas technology to develop virus-research plants, investigate the relationship between photoperiod and metabolism or present a method for assessment of protein S-nitrosylation. Fourthly is a paper that includes a contribution from the University of Leeds that investigates the evolutionary and functional relationship of the WOX gene family. Finally is a study that highlights the role of the AUGMIN complex during microtubule activity that includes a contribution from the University of Leicester.

In addition, although not involving Arabidopsis, we should mention an exciting study from Gerben van Ooijen (Edinburgh) that has discovered a conserved circadian mechanism based on magnesium rhythms that is linked to energy expenditure.

Ge Y, Cai YM, Bonneau L, Rotari V, Danon A, McKenzie EA, McLellan H, Mach L, Gallois P (2016) Inhibition of cathepsin B by caspase-3 inhibitors blocks programmed cell death in Arabidopsis. Cell Death Differ. http://dx.doi.org/10.1038/cdd.2016.34 Open Access

The corresponding author of this paper is Patrick Gallois from the University of Manchester and includes contributions from Hazel McLellan in Dundee almongside Chinese and Austrian collaborators. This study investigates the role of caspase proteins on control of programmed cell death in plants. This research area has been hindered by the apparent lack of plant caspase orthologues despite pharmacological evidence that proteins with caspase activity are active in plants. The authors use a labeled caspase-3 inhibitor to identify the Arabidopsis Cathepsin B3 (AtCathB3) protein as having caspase activity, which was verified using recombinant proteins during in vitro enzyme assays. AtCathepsinB1,2,3 triple mutant plants demonstrate a reduction in PCD induced by different stresses and explains why caspase inhibitors are effective tools for studying PCD in plants. The core Cathepsin B protein is evolutionarily conserved suggesting that an ancestral pathway exists that controls PCD, the details of which require further study.

Maxwell DJ, Partridge JC, Roberts NW, Boonham N, Foster GD (2016) The Effects of Plant Virus Infection on Polarization Reflection from Leaves. PLoS One. 11(4):e0152836 http://dx.doi.org/ 10.1371/journal.pone.0152836 Open Access

Gary Foster’s research group at the University of Bristol collaborate with others at the University of York and in Australia for this study that investigates how plant viruses may modify gene expression to benefit their own transmission. They show that Potato virus Y and Cucumber mosaic virus (CMW), which both are transmitted by aphids, significantly reduce the amount of polarised light that is reflected from abaxial leaf surfaces of tobacco plants particularly when compared to the effects caused by non-insect vectored viruses. However this effect was not shown in Arabidopsis leaves infected by a variety of differently transmitted viruses. Interestingly ECERIFERUM6 (CER6) transcripts accumulate to higher levels following infection with insect vectored viruses and as this gene is involved in cuticle wax synthesis the authors suggest that induced changes in cuticle composition might be key in understanding how viruses encourage predation by their insect vectors. Finally the authors discuss the overall adaptive significance of these results.

Drake T, Keating M, Summers R, Yochikawa A, Pitman T, Dodd AN (2016) The Cultivation of Arabidopsis for Experimental Research Using Commercially Available Peat-Based and Peat-Free Growing Media. PLoS One. 11(4):e0153625 http://dx.doi.org/ 10.1371/journal.pone.0153625 Open AccessPeatPic

GARNet committee member Anthony Dodd, also from the University of Bristol, leads this study into the growth of Arabidopsis on peat-free media, which was motivated by the unsustainable use of peat-based composts. They found that biomass accumulation and seed yield were reduced on peat-free media and that some types of this media was more suspectible to fungal contamination. Overall vegetative phenotypic parameters were similar between plants grown on peat-based or peat-free media, indicating that this type of media will be appropriate for future analysis. However the seed yield was usually reduced, indicating that experiments looking at post-phase change phenotypes might not be as comparable between plants growth on media with different amount of peat.

Pyott DE, Sheehan E, Molnar A (2016) Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants Mol Plant Pathol. http://dx.doi.org/10.1111/mpp.12417

Attila Molnar (Edinburgh) is the corresponding author on this study that uses the transformative technology CRISPR/Cas9 to engineer Arabidopsis plants that are resistant to potyvirus infection. This is achieved by targeting the genes encoding the translation initiation factor eIF(iso)4E that had been previously identified as being critical for viral establishment. Importantly they subsequently selected transgene-free plants that have no phenotypic changes when compared to wildtype growth under standard conditions. As the potyvirus Turnip Mosaic Virus is an important pathogen for vegetable crops this is potentially an extremely powerful technique for generating virus-resistance food crops.

Flis A, Sulpice R, Seaton DD, Ivakov AA, Liput M, Abel C, Millar AJ, Stitt M (2016) Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis Plant Cell Environ. http://dx.doi.org/10.1111/pce.12754

This German–led study aims to connect the expression of photoperiod-length responsive circadian clock-regulated genes with those involved in metabolic processes such as starch degradation and includes a contribution from Professor Andrew Miller from the Edinburgh SynthSys Centre. The authors assess global gene expression by transcript profiling at photoperiods ranging from 4-18 hours and found that changes in transcript abundance at dawn throughout these photoperiods were as large as changes seen in individual experiments when comparing dawn and dusk. These complex interactions revealed coordinated regulation of key metabolic processes and begins to demonstrate how metabolism is linked to photoperiod.

Homem RA, Le Bihan T, Yu M, Loake GJ (2016) Identification of S-Nitrosothiols by the Sequential Cysteine Blocking Technique Methods Mol Biol. 1424:163-74. http://dx.doi.org/10.1007/978-1-4939-3600-7_14

This paper from the lab of Gary Loake (Edinburgh) describes the methods they use to investigate the role of protein S-nitrosylation in the immune responses of Arabidopsis. These are based on a modification of the biotin-switch technique, which they term sequential cysteine blocking.

Dolzblasz A, Nardmann J, Clerici E, Causier B, van der Graaff E, Chen J, Davies B, Werr W, Laux T (2016) Stem cell regulation by Arabidopsis WOX genes Mol Plant. S1674-2052(16)30029-6 http://dx.doi.org/10.1016/j.molp.2016.04.007

This German-led study includes work from the lab of Brendan Davies at the University of Leeds and investigates the role of the WUSCHEL-RELATED HOMEOBOX (WOX) transcription factor gene family during stem cell development and maintenance. Most members of the WUS-clade can largely substitute for WUSCHEL activity in the shoot meristem, which is absolutely dependent on a conserved WUS-box motif that is critical for the interaction with TOPLESS co-repressors. In contrast to the WUS clade, the WOX13 and WOX9 clades cannot substitute for WUS activity. The indicates that WOX control of shoot and floral meristem relies on certain currently not-fully-understood attributes of the WUS-clade of proteins.

Oh SA, Jeon J, Park HJ, Grini PE, Twell D, Park SK (2016) Analysis of gemini pollen 3 mutant suggests a broad function of AUGMIN in microtubule organization during sexual reproduction in Arabidopsis Plant J. http://dx.doi.org/10.1111/tpj.13192

David Twell (Leicester) is an author on his Korean-led study that reports on the identification of the new gem3 mutant, which displays defects in gametophytic development. Mutant plants exhibits disrupted cell division during male meiosis, at pollen mitosis I and throughout female gametogenesis. Gem3 is a hypomorphic allele of the AUGMIN subunit 6 gene, which is a component of Augmin complex responsible for microtubule (MT) nucleation in acentrosomal cells. In the gem3 mutant, the authors show that MT arrays are incorrectly distributed, likely causing the gametophyte-specific phenotypes and demonstrating a broad role for the augmin complex during sexual reproduction in flowering plants

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