29th Jan 2016

This weeks Arabidopsis Research Roundup features a paper from David Baulcombe and Joe Ecker that further deciphers mechanisms of RNA silencing and is kindly discussed by postdoc Mat Lewsey in a short audio description. Elsewhere there are three studies that include researchers from CPIB in Nottingham. Leah Band contributes to a study that links environment sensing, cell death and auxin signaling whilst Ive De Smet leads a study that finds new proteins involved in cell division. Malcolm Bennett and John King take a modeling approach to describe auxin signaling via the GH3 protein family. Finally Frank Menke leads a study that provides more detail into Pattern Recognition Receptor (PRR) mediated immune signaling and then Jim Dunwell participates in a paper that describes a new method of analyzing GWAS data.

Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR (2016) Mobile small RNAs regulate genome-wide DNA methylation. Proc Natl Acad Sci U S A. Open Access

Over the past few years RNA-mediated silencing has emerged a key mechanism for the control of gene expression. This study is a collaboration between the lab of Sir David Balcombe (Cambridge) and Joe Ecker at the SALK institute in California. Mat Lewsey, who is a British postdoc working with Professor Ecker, kindly provided a short audio description of the paper. These groups have previously shown that sRNAs are highly mobile throughout the plant. This study shows that thousands of loci expressed in roots are dependent on mobile sRNAs generated from the shoot. They unpick the genetic basis of this response showing that it is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) but not CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. They also show that mobile sRNAs are resposible for the silencing of TEs that are found in gene-rich regions, although this is not a physiologically important response in Arabidopsis, which contains a relatively small amount of transposon tissue. Interestingly they a show that sRNAs generated from different Arabidopsis ecotypes are able to move across graft junctions and can cause methylation in usually unmethylated regions.

Xuan W, Band LR, Kumpf RP, Van Damme D, Parizot B, De Rop G, Opdenacker D, Möller BK, Skorzinski N, Njo MF, De Rybel B, Audenaert D, Nowack MK, Vanneste S, Beeckman T (2016) Cyclic programmed cell death stimulates hormone signaling and root development in Arabidopsis. Science . 351(6271):384-7

This study is led by Tom Beeckman from Gent University and features Leah Band from CPIB in Nottingham. They reveal an exciting relationship between cell death in root cap cells and hormone signaling. The root cap is a protective tissue that overlies the Arabidopsis root tip and might be considered as an ‘inactive’ tissue. However this study shows that an auxin signal released from root cap cells sets the spacing of lateral organs along the root. As root cap cells move up the root they undergo programmed cell death, which in turn releases a pulse of auxin and establishes a pattern of lateral root formation. The authors suggest that this relationship might integrate external soil conditions so that lateral roots will develop to optimise uptake of water and nutrients. It is well known that an auxin signal simulates lateral root formation but this study provides an explanation as to the genesis of this signal and its integration with external environmental factors.

Yue K, Sandal P, Williams EL, Murphy E, Stes E, Nikonorova N, Ramakrishna P, Czyzewicz N, Montero-Morales L, Kumpf R, Lin Z, van de Cotte B, Iqbal M, Van Bel M, Van De Slijke E, Meyer MR, Gadeyne A, Zipfel C, De Jaeger G, Van Montagu M, Van Damme D, Gevaert K, Rao AG, Beeckman T, De Smet I (2016) PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root. Proc Natl Acad Sci U S A.

This broad collaboration between US-UK and Belgian researchers is led by Tom Beeckman and Ive De Smet, who works at CPIB in Nottingham. In addition it includes a contribution from Cyril Zipfel at TSL. This study aimed to identify proteins that interact with the plasma membrane-localized receptor kinase ARABIDOPSIS CRINKLY 4 (ACR4), which plays a role in the control of cell division in the Arabidopsis root. They find that PROTEIN PHOSPHATASE 2A-3 (PP2A-3), a catalytic subunit of PP2A holoenzymes interacts with ACR4 and has a previous uncharacterised role in control of formative cell divisions. The authors show that the biochemical network that links ACR4 and PP2A-3 is regulated by phosphorylation.

Mellor N, Bennett MJ, King JR (2016) GH3-Mediated Auxin Conjugation Can Result in Either Transient or Oscillatory Transcriptional Auxin Responses. Bull Math Biol.

This paper led by Professor Malcolm Bennett and John King from CPIB is an example of the growing number of multi-disciplinary interactions between biologists and mathematicians. Here a model is developed that interrogates auxin signaling and homeostasis through the GH3 gene family. This includes a parameter that considers auxin transport via the LAX3 influx protein, which, together with the activity of GH3 proteins can facilitate a positive feedback loop that allows cells to response to excess auxin.

Mithoe SC, Ludwig C, Pel MJ, Cucinotta M, Casartelli A, Mbengue M, Sklenar J, Derbyshire P, Robatzek S, Pieterse CM, Aebersold R, Menke FL (2016) Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase. EMBO Rep. Open Access

Frank Menke (TSL, Norwich) is the leader on this collaboration between UK, Dutch and Swiss researchers that investigates innate immunity signaling mediated via Pattern Recognition Receptors (PRRs). Tight control of this signalling is very important to prevent spurious activation of the immune response. These authors find that the differentially phosphorylated MKKK7 can interact with the FLS2 protein, which is key in the perception of bacterial flagellin. In turn MKKK7 attenuates the signalling of a downstream MAPK that contributes to defence-related gene expression. Therefore the show that the FLS2-MKKK7 signaling module is critical for control of innate immunity.

Wang SB, Feng JY, Ren WL, Huang B, Zhou L, Wen YJ, Zhang J, Dunwell JM, Xu S, Zhang YM (2016) Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology. Sci Rep. Open Access

Professor Jim Dunwell (Reading) is a UK contributor to this largely Chinese publication that introduces a new method to analysis GWAS-style data. They propose an analysis based on random-SNP-effect MLM (RMLM) and a multi-locus RMLM (MRMLM) and using stimulations show that their new method can be powerful than conventional types of analysis. To test the method they analysed flowering time traits in Arabidopsis and detected more genes that were involved in the process.

For those interested in different-types of GWAS analysis, Professor David Salt introduced another new method during a recent ARR.