GARNet Research Roundup: April 27th

This weeks GARNet research roundup features four papers that include Malcolm Bennett (University of Nottingham) as an author. The first three are linked manuscripts that investigate the role of auxin on root hair development that is controlled by varying phosphate levels. Ranjan Swarup provides an audio summary of two of these papers on the GARNet YouTube and podcast feeds.

The fourth paper from Nottingham is a collaboration with GARNet PI Jim Murray (Cardiff University) that characterises the STM gene network and its influence on meristem development.

The fifth paper from the lab of Paul Dupree in Cambridge characterises the stem transcriptome whilst the next paper from Iain Johnston and George Bassel (University of Birmingham) identifies a bet-hedging network that influences seed germination. The final paper features Seth Davies (University of York) as a co-author and investigates the impact of changes in circadian rhythms on short architecture.


Researchers at the University of Nottingham are involved in three back-to-back papers that add a mechanistic framework to the relationship between phosphate and auxin signaling in root hairs.

Bhosale R, Giri J, Pandey BK, Giehl RFH, Hartmann A, Traini R, Truskina J, Leftley N, Hanlon M, Swarup K, Rashed A, Voß U, Alonso J, Stepanova A, Yun J, Ljung K, Brown KM, Lynch JP, Dolan L, Vernoux T, Bishopp A, Wells D, von Wirén N, Bennett MJ, Swarup R (2018) A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate. Nat Commun. 9(1):1409. doi: 10.1038/s41467-018-03851-3

https://www.nature.com/articles/s41467-018-03851-3

Open Access

The first paper is led by Ranjan Swarup and defines components of auxin biosynthetic, transport and signaling pathways that are involved in the change root hair development in response to different phosphate concentrations in Arabidopsis. Ranjan discusses this paper on YouTube.

Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ (2018). Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate. Nat Commun. 9(1):1408. doi: 10.1038/s41467-018-03850-4

https://www.nature.com/articles/s41467-018-03850-4

Open Access

This paper led by Malcolm Bennett uses a rice model to investigate the relationship between auxin and root hair elongation in response to low concentrations of phosphate. They show rice aux1 mutants have significant changes in root architecture.

Dindas J, Scherzer S, Roelfsema MRG, von Meyer K, Müller HM, Al-Rasheid KAS, Palme K, Dietrich P, Becker D, Bennett MJ, Hedrich R (2018) AUX1-mediated root hair auxin influx governs SCF(TIR1/AFB)-type Ca(2+) signaling. Nat Commun. 9(1):1174. doi: 10.1038/s41467-018-03582-5

Open Access

The third paper includes Malcolm Bennett as a co-author and investigates how the auxin transport and signaling pathways stimulate calcium signaling during root hair elongation.


Scofield S, Murison A, Jones A, Fozard J, Aida M, Band LR, Bennett M, Murray JAH (2018) Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network. Development pii: dev.157081. doi: 10.1242/dev.157081

http://dev.biologists.org/content/early/2018/04/12/dev.157081.long

Open Access
GARNet PI Jim Murray is the corresponding author on this manuscript that is led by Dr Simon Scofield and includes collaborators from the University of Nottingham. They have explored the gene regulatory network that is regulated by the key meristem identity gene SHOOT MERISTEMLESS (STM). This network includes an over-representation of transcription factor families, each of which have distinct roles in meristem development. They use in planta experimentation and in silico modeling to investigate the relationship between STM and CUC1 in more detail. Overall this study confirms that STM is a central regulator of shoot meristem function.


Faria-Blanc N, Mortimer JC, Dupree P (2018) A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis. Front Plant Sci. 9:384. doi: 10.3389/fpls.2018.00384

Open Access

Paul Dupree (University of Cambridge) is the corresponding author of this study that uses a range of Arabidopsis cell wall mutants to investigate the stem transcriptome. In plants with defects in xylan synthesis the authors found surprisingly few transcriptional changes. This indicates that once plants have committed to a terminal secondary cell wall program there is little need for transcriptional changes even after cell wall damage.


Johnston IG, Bassel GW (2018) Identification of a bet-hedging network motif generating noise in hormone concentrations and germination propensity in Arabidopsis. J R Soc Interface. 15(141). pii: 20180042. doi: 10.1098/rsif.2018.0042.

Open Access
Iain Johnston (University of Birmingham) leads this study that has identified a bet-hedging network that links hormone signaling during Arabidopsis germination. This type of network allows plants to more easily adapt to varying environmental conditions but can preclude maximum growth. In this system the network is based upon the regulation of ABA synthesis, activity and degradation, which is maintained at a constant mean level even though it exhibits significant noise. They investigate the parameters that might be tweaked to reduce variation in germination rate and therefore might be targets for modification in order to maximise responses under particular environmental conditions.

George Bassel who is a co-author on this paper will be speaking at the GARNet2018 Meeting in York in September.

http://rsif.royalsocietypublishing.org/content/15/141/20180042.long

Rubin MJ, Brock MT, Baker RL, Wilcox S, Anderson K, Davis SJ, Weinig C (2018) Circadian rhythms are associated with shoot architecture in natural settings. New Phytol. doi: 10.1111/nph.15162.

Seth Davies (University of York) is a co-author on this study that assesses the effect of circadian rhythms on aerial phenotypes that lead to fruit production in field grown Arabidopsis. This was assessed over two growing seasons and they show that variation in clock function significantly impacts shoot architecture.

Ranjan Swarup talks to GARNet

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Published on: April 23, 2018

Ranjan Swarup (University of Nottingham) discusses a couple of recent papers published in Nature Communications that describe the relationship between phosphate and auxin signaling in the roots of Arabidopsis and rice plants.

https://www.nature.com/articles/s41467-018-03851-3

https://www.nature.com/articles/s41467-018-03850-4

GARNet Research Roundup: April 11th 2018

This weeks GARNet research roundup begins with a microscopy-based study led by Lorenzo Frigerio from the University of Warwick that investigates the origin of Protein Storage Vacuoles. The second paper from John Doonan at Aberystwyth University looks at how differential splicing of cyclin-dependent Kinase G1 effects the thermosensory response. Reiner van de Hoorn from Oxford leads the next paper that characterises the use of activity-based protein profiling (ABPP) to identify novel α-glycosidases in model and non-model plants. Simon McQueen-Mason from York is corresponding author of the next paper that identified a new QTL from Brachypodium that is involved in cell wall formation. The fifth paper is led by Anthony Dodd from Bristol and characterises the role of the SnRK1 complex in hypocotyl elongation whilst the penultimate manuscript from Julia Davies’s lab in Cambridge performs patch clamp analysis of dorn1 mutant plants. The final paper from Brendan Davies at the University of Leeds characterises the SMG kinase, a gene that is lacking from the Arabidopsis genome, in Physcomitrella patens.


http://www.plantphysiol.org/content/early/2018/03/19/pp.18.00010.long

Feeney M, Kittelmann M, Menassa R, Hawes C, Frigerio L. Protein storage vacuoles originate from remodelled pre-existing vacuoles in Arabidopsis thaliana (2018) Plant Physiol. 2018 Mar 19. pii: pp.00010.2018. doi: 10.1104/pp.18.00010 Open Access

This collaboration between the Universities of Warwick and Oxford Brookes is led by Lorenzo Frigerio and Chris Hawes. They have investigated the origin of seed Protein Storage Vacuoles (PSV) using a two-pronged approach using confocal and immunoelectron microscopy. They looked at embryo development as well as in leaf cells that have been reprogrammed for embryonic cell fate by overexpression of the LEAFY COTYLEDON2 TF. These studies indicate that PSVs are formed following the reprogramming of pre-existing embryonic vacuole (EV) rather than from de novo assembly.


https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.13914

Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan JH. The Cyclin Dependent Kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A (2018) Plant J. doi: 10.1111/tpj.13914 Open Access

John Doonan (Aberystwyth University) is the corresponding author on this UK-Austrian collaboration that presents the role of the cyclin-dependent Kinase G1 (CDKG1) in thermosensing in Arabidopsis. Ambient temperature change causes altered gene expression of the spliceosome component, ATU2AF65A. Interestingly the CDKG1 gene is differentially spliced and to produces two protein isoforms that are both needed to complement the expression of ATU2AF65A across a temperature range. This alternative splicing is dependent on CDKG2 and CYCLIN L1 and is a novel control mechanism in the temperature control response.


Husaini AM, Morimoto K, Chandrasekar B, Kelly S, Kaschani F, Palmero D, Jiang J, Kaiser M, Ahrazem O, Overkleeft HS, van der Hoorn RAL (2018) Multiplex fluorescent, activity-based protein profiling identifies active α-glycosidases and other hydrolases in plants. Plant Physiol. pii: pp.00250.2018. doi: 10.1104/pp.18.00250 Open Access

Renier Van de Hoorn (University of Oxford) leads this pan-european study that uses novel cyclophellitol aziridine probes that label α-glycosidase enzymes. They identified two novel α-glycosidases in Arabidopsis as well as using the technique in non-model saffron crocus. Finally they showed that this multiplex fluorescent labelling in combination with probes for serine hydrolases and cysteine proteases can be used to identify changes in hydrolase activity in response to pathogen infection.


Whitehead C, Ostos Garrido FJ, Reymond M, Simister R, Distelfeld A, Atienza SG, Piston F, Gomez LD, McQueen-Mason SJ (2018) A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon. New Phytol. doi: 10.1111/nph.15089 Open Access

Simon McQueen-Mason (University of York) leads this study that use QTL mapping to identify a gene in Bracypodium that is involved in cell wall architecture, which might then be a target to develop plants with improved cellulose digestibility. This glycosyl transferase family (GT) 43 protein is an orthologue of Arabidopsis IRX14, which is involved in xylan biosynthesis. When RNAi was used to reduce expression of this gene the resulting plants showed increased digestibility, indicating that this BdGT43A will be a good target for future breeding plans.


Wang L, Wilkins KA, Davies JM (2018) Arabidopsis DORN1 extracellular ATP receptor; activation of plasma membrane K(+) -and Ca(2+) -permeable conductances New Phytol. 2018 Mar 25. doi: 10.1111/nph.15111. Open Access

This letter to New Phytologist from the lab of Julia Davis (University of Cambridge) outlines some experiments to determine whether the DORN1 plasma membrane receptor is responsible for transmitting a signal from extracellular ATP (eATP). They performed patch clamp analysis on isolated protoplasts and showed that DORN1 is involved in the activation of Ca+ and K+ pumps by eATP as, in contrast to wildtype, dorn1 mutant protoplast showed no voltage changes after incubation with eATP.


Simon NML, Sawkins E, Dodd AN. Involvement of the SnRK1 subunit KIN10 in sucrose-induced hypocotyl elongation (2018) Plant Signal Behav. 27:1-9. doi: 10.1080/15592324.2018.1457913.

Anthony Dodd (University of Bristol) is the corresponding author of this follow-on study from one that previously featured on the GARNet YouTube channel. This study measures sucrose-induced hypocotyl elongation in two T-DNA mutants of the SnRK1 subunit KIN10 gene. These mutants had altered responses to sucrose leading to the hypothesis that the SnRK1 complex suppresses hypocotyl elongation in the presence of external sugar.


Lloyd JPB, Lang D, Zimmer AD, Causier B, Reski R, Davies B (2018) The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Res. doi: 10.1093/nar/gky225 Open Access

Brendan Davis (University of Leeds) is the corresponding author on research that investigates the role of the SMG1 kinase during nonsense-mediated mRNA decay (NMD) in the moss Physcomitrella patens. This kinase plays a critical role in animals but as it is not present in Arabidopsis, its function is not well studied in plants. However moss smg mutants show expression changes in genes involved in a variety of processes indicating that NMD is a common control mechanism in moss. In addition these plants have increased susceptibility to DNA damage, which suggests that the SMG1 kinase is a key player in quality control mechanisms in plants.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky225/4955258
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