July 1 at ICAR

July 1 at ICAR 2016

Caveat emptor – today was a long day and I’m tired, but I’m sharing my notes from today’s talks (at least the ones I attended) for those of you who are interested. As before, check out the Twitter stream for additional insights (and nice photos) from the talks. If you spot a typo or error, please let me know and I’ll correct it. Also, if you were at the talks or are a speaker and have additional insights, or if you want to share notes from the talks I wasn’t able to attend, I’d be happy to add them.

For what they’re worth, enjoy! And Happy Friday!

Today started with two concurrent sessions, Embryogenesis and Abiotic Stress

Session 9 (Development – Embryogenesis)

Dolf Weijers (Wageningen University, Netherland) – The Arabidopsis embryo as a model for understanding the genetic basis for multicellular development

Dolf showed beautiful 3D imaging of Arabidopsis embryos to map each cell and cell division during embryogenesis, using wild-type and mutant lines. They also did transcriptomic analysis of 8 and 16 cell Arabidopsis embryos (these things are seriously tiny… well done). One observation is that many of the overrepresented genes are involved in the actin cytoskeleton and cell wall formation. They’ve also created a soon-to-be released library of cell biology markers for early embryogenesis. They’re now also mapping the cytoskeleton of individual cells of these early embryos. Additional studies focus on the role of auxin in embryogenesis – see Different auxin response machineries control distinct cell fates in the early plant embryo for background. He showed some lovely experiments studying the effects of altered cell-specific auxin responses, concluding there are multiple, local, MONOPTEROS-dependent auxin responses. He then introduced SOSEKI protein family, that localizes to the corners of cells. Recent reviews of the groups findings (and associated references) can be found in Tissue and Organ Initiation in the Plant Embryo: A First Time for Everything and Transcriptional Responses to the Auxin Hormone.

Stewart Gilmor (Irapuato, Mexico) – Zygotic genome activation in isogenic and hybrid embryos of Arabidopsis.

Stewart introduced “delayed zygotic genome activation” in development – the process by which the earliest stages of embryogenesis are controlled by maternal genes / transcripts. This model comes from animals, and so Stewart addressed the question of whether this occurs in plants as well. As background, segregation of embryo defective genes shows 25% lethality, suggesting zygotic control. However, some studies indicated that for some genes only the maternal allele is expressed in early embryogenesis. See for example  Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis and Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos. Here’s a key paper of Stewart’s work Non-equivalent contributions of maternal and paternal genomes to early plant embryogenesis and a nice review article summarizing the state of the field Zygotic genome activation in isogenic and hybrid plant embryos

Minako Ueda (Nagoya University, Japan) –Live-cell imaging of the intracellular dynamics underlying the zygote polarization in Arabidopsis.

Minako introduced zygote polarity, using live-imaging of intracellular dyanics, and chemical screening – see Live-Cell Imaging and Optical Manipulation of Arabidopsis Early Embryogenesis for the amazing method they have developed. She showed images of mitochondrial movement and division, and how it changes with nuclear division, in a zygote stage-specific manner. She next showed chemical screening for polarity regulation. Different chemicals interfere with embryo polarity at different stages, allowing her to diagram several stages in the progression from an asymmetric cell to a polar cell. The work is still unpublished (you should have been here).

Gwyneth Ingram (RDP-Lyon, France) – A defence-related inter-compartmental signalling pathway regulates embryonic cuticle integrity in Arabidopsis

Gwyneth describes the formation of the embryo cuticle – de novo formation of a barrier. Several genes have previously been identified that are required for this process – see ZHOUPI controls embryonic cuticle formation via a signalling pathway involving the subtilisin protease ABNORMAL LEAF-SHAPE1 and the receptor kinases GASSHO1 and GASSHO2. Interestingly, these genes are expressed in different compartments some in the endosperm and some in the embryo. Interestingly, the genes promote the expression of “defense associated markers” – perhaps not totally surprising as the closest relatives of GSO1 and 2 are PEPR1 and 2, involved in pathogen responses. Suggests that a defence signalling pathway has been hijacked to provide an autoimmune-type response?


Session 10 (Abiotic Stress 1)

Zhizhong Gong (China Agricultural University, China) – Regulation of the ABA co-receptor PP2Cs

Erwin Grill (Technische Universität München, Germany) – Exploring abscisic acid receptors for water productivity

Shuhua Yang (China Agricultural University) – Regulation of protein kinases in plant response to cold stress

Pedro Rodriguez (CSIC, Spain) – New mechanisms for modulation of ABA receptor function and ABA signalling


After coffee:

Session 11 (Development – Reproductive and flowering)

Richard M. Amasino (University of Wisconsin-Madison, U.S.A) -Flowering pathways in Arabidopsis compared to those in other groups of plants.

Ilha Lee (Seoul National University, Korea) – Mechanism of transcriptional regulation of VIN3, a key player of vernalization-induced epigenetic silencing in Arabidopsis

Yu Hao (National University of Singapore, Singapore) – Regulation of florigen transport in Arabidopsis

Doris Wagner (University of Pennsylvania, U.S.A) – Cis- and trans-determinants of Polycomb Repressive Complex 2 recruitment in Arabidopsis

Session 12 (Abiotic Stress 2)

Dae-Jin Yun (Gyeongsang National University, Korea) A novel thiol-reductase activity of Arabidopsis YUC6 confers drought tolerance independently of auxin biosynthesis

Dae-Jin described studies that show that the YUCCA6 gene has an auxin-independent function in conferring drought tolerance. YUC6 contains a previously unrecognized FAD- and NADPH-dependent thiol-reductase activity (TR). Experiments show that the role of YUC6 in conferring drought tolerance is independent of auxin biosynthesis. Its drought-tolerance conferring role is mediated by its effects on ROS control under oxidative stress. However, new data show that The Thiol Reductase Activity of YUCCA6 Mediates Delayed Leaf Senescence by Regulating Genes Involved in Auxin Redistribution. Interestingly, ROS accumulation reduces auxin efflux transporter levels. Due to both its auxin effect and drought-tolerance effect, YUCCA6 shows promise as an agronomically important gene.

José Manuel Pardo Prieto (IRNAS-CSIC, Spain) – Regulation of potassium uptake and storage

José introduces how plants take up and regulate the uptake of K+, an essential macronutrient. Furthermore, K+ uptake is extremely critical for tolerance to Na+ as well as to maintain cell turgor (see Ion exchangers NHX1 and NHX2 mediate active potassium uptake into vacuoles to regulate cell turgor and stomatal function in Arabidopsis). Plants have a family of regulated K+ transporters, of both low- and high- affinity. Previously,  José‘s lab showed that CIPK23 regulates HAK5-mediated high-affinity K+ uptake in Arabidopsis roots. Their most recent work, newly out in Plant Physiology, shows that A Single Amino Acid Substitution in the Sodium Transporter HKT1 Associated with Plant Salt Tolerance.

Motoaki Seki (RIKEN, Japan) – Novel Epigenetic, RNA and Peptide Regulation in Plant Abiotic Stress Responses

Motoaki showed that epigenetic factors contribute to plant abiotic stress responses. See Transition of chromatin status during the process of recovery from drought stress in Arabidopsis thaliana and Ky-2, a Histone Deacetylase Inhibitor, Enhances High-Salinity Stress Tolerance in Arabidopsis thaliana for recent work. He also showed the results from his latest paper on the role of RDR genes, which should be out very soon!

Dong Liu (Tsinghua University, China) – Arabidopsis ALUMINUM SENSITIVE3 mediates phosphate deficiency-induced remodeling of root architecture by modulating root iron homeostasis

Dong described the effects of nutrient deficiency on root system architecture. See also Arabidopsis PHL2 and PHR1 Act Redundantly as the Key Components of the Central Regulatory System Controlling Transcriptional Responses to Phosphate Starvation.

Kenji Miura (University of Tsukuba, Japan) – Functional analysis of ICE1 interacting proteins for cold tolerance

Kenji identified a role for transcription factors ICE1, MYC67 and 70 in regulation of CBF3 genes. In cold, ICE1 replaces MYC at promoter binding sites. CML10 and 12 are involved in cold tolerance. Model: cold leads to calcium release, interacts with calmodulin-like protein, interacts w/ ICE1 to promote binding. See http://www.gene.tsukuba.ac.jp/~kmiura/publication2012.htm and http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634503/



Session 13 (Hormone-CK, Auxin)

Sabrina Sabatini (Università di Roma La Sapienza, Italia) – An Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root

Balancing growth and meristem maintenance in root meristem – model for an antagonistic interaction between cytokinin and auxin (see http://science.sciencemag.org/content/322/5906/1380.abstract). But the carefully constructed model failed to show the rise of auxin levels again behind the root tip. Tracked down the need to incorporate auxin cojugation/ inactivation via GH3 gene family in the model. They found an auxin minimum behind the root tip is critical for cells to passage into their next developmental stage (differentiation). The position of the auxin minimum always correlates with the transition zone. Cytokinin controls the position of the auxin minimum, thus setting meristem size. Used R2D2 reporter which is really lovely.

Ari Pekka Mähönen (University of Helsinki, Finland) – Elucidating cell fate decisions in the Arabidopsis root cambium

Arabidopsis root is a good model for the study of vascular cambium and secondary growth (wood). The radial pattern is specified at the tip. Nothing much happens for a few days, then the cambium is activated and secondary growth begins. Did clonal analysis / lineage tracing to determine where cells originate. Physical contact w existing xylem is important for cambium formation. Xylem pole pericycle cells can differentiate into many other cell types, including lateral roots and the secondary growth. Therefore, these two different possible cells for these xylem-pole pericycle (XPP) cells. Interestingly, cambial cell divisions in XPP cells prevent auxin-induced lateral root formation. It’s either or. Cytokinins are required and sufficient for cambium activation. Note that in cytokinin deficient mutants you get no cambium development. Increased cytokinin signalling in XPP cells correlates with activation of cambium. Conclusion – auxin / cytokinin ratio is important in determining the balance between secondary growth and branching.

Lars Ostergaard (John Innes Centre, U.K) – Auxin acts on a transcription-factor complex to direct symmetry in the gynoecium

Early work showed that some auxin mutants show abnormal gynoecia. IND and ETTIN are both transcription factor that bind auxin response elements and regulate pinoid. IND is very specific to fruit development, but ETTIN has many roles in development. (Battery died during talk!) See http://www.nature.com/nature/journal/v459/n7246/abs/nature07875.html for background on this work.

Hitoshi Sakakibara (RIKEN, Japan) – Regulation of cytokinin biosynthesis and transport in response to nutritional changes

Plant growth is modulated by environment to optimize nutrient uptake and therefore growth potential. Hitoshi works on cytokinin biosynthesis and transport. His work has elucidated how high N restricts root growth, and he has new data showing how elevated CO2 promotes leaf and shoot growth via upregulation of CK biosynthesis genes in roots. (in revision). The metabolic signal for the high CO2 response is sugar produced by increased photosynthesis. Sugars and gln transported in the phloem and form a metabolic signal. Transport of root derived tZ and tZR sensitive to N condition – both active and inactive form translocated, but their ratio changes.

Session 14 (Plant-Microbe Interaction 1)

Ding Zhong Tang (Chinese Academy of Science, China) – Dissection of the molecular mechansims of exo70B1-activated plant defense responses

Ping He (Texas A&M University, U.S.A) – Protein poly(ADP-ribosyl)ation in Arabidopsis innate immunity

Yuelin Zhang (University of British Columbia, Canada) – Regulation of two master regulators of plant immunity in defense against pathogens

Roger Innes (Indiana University Bloomington, U.S.A) – Expanding the Recognition Specificity of a Plant Disease Resistance Genes Using Decoys


Session 15 (Hormone – GA, BR, Ethylene)

Zhiyong Wang (Stanford University, U.S.A) – Balance Growth with Carbon Availability through Crosstalk between Sugar-TOR and BR Signaling Pathways

Ildoo Hwang (POSTECH, Korea) – Regulatory aspects of glycogen synthase kinases on auxin signaling during vasculature development

David Alabadi (Instituto de Biologia Molecular y celular de plantas, Spain) – Gibberellins control xylem development through DELLA-SACL1 interaction

Hong Qiao (University of Texas-Austin, U.S.A) – Study the function of EIN2 C-terminus in the nucleus in ethylene response


Session 16 (Plant Microbe Interaction 2)

Note – Morgan Halane (@themorgantrail) did a great job Tweeting all of the Plant-Microbe talks so please see his Twitter stream for better coverage than I was able to record….)

Jonathan Jones (The Sainsbury Laboratoy, U.K) – Functional dissection of paired immune receptor complexes in plants.

Interactions between plants and bacterial effectors Rps4 resistance gene. RRS1 is a recessive R gene linke to RPS4. The two proteins diverge at c-term. RRS1 has a WRKY-DNA binding domain. The recognition by RPS4/RRS1 complex involves RRS1 WRKY domain. Maybe their function is to recoginze effectors that target WRKYs? A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors. See also Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens

Gitta Coaker (UC-Davis, U.S.A) – Kinase-Mediated Stabilization of Plant Immune Signaling

Gitta introduces the cytoplasmic kinases that operate downstream R genes. Receptor like cytoplasmic kinases are involved in PTI and ETI. Example BIK1, also PBL13. SIK1 kinase is part of the Map4 kinase family. Today Coaker is talking about SIK1 a conserved member of MAP4 family. sik1 T-DNA insertion mutants are stunted in growth and have high SA levels.  sik1 mutants are compromised in RPS5-mediated hypersensitive response. sik1 mutants have a reduced ROS phenotype similar to bik1 mutants.

Ryohei Terauchi (Iwate Biotechnology Institute, Japan) – Arms race coevolution between pathogen and plant: The case of Magnaporthe oryzae AVR-Pik effector and rice heavy metal associated (HMA) domain proteins

Ryohei works on a rice pathogen. Avirulence genes were cloned in 2009. Today’s talk is on AVR-Pik. http://www.plantcell.org/content/21/5/1573.abstract. The gene shows hyperaccumulation of variation, consistent with strong selection. 2012 They found “Arms race co-evolution of Magnaporthe oryzae AVR-Pik and rice Pik genes driven by their physical interactions.” The structure of the interaction between Pikp1-HMA and AVR-Pik was published last year in eLife Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor. sHMA may be involve in ROS regulation.

Sheng Yang He (Michigan State University, U.S.A) – Bacterial pathogenesis: Toward reconstitution in a model plant-pathogen system

Sheng Yang works on the Arabidopsis – Pseudomonas syringae interaction, a “model plant-pathogen interaction”. For his good 2013 review, see Pseudomonas syringae pv. tomato DC3000: A Model Pathogen for Probing Disease Susceptibility and Hormone Signaling in Plants. Question – is PTI enough for immunity A – No. Limitations of study: growth chamber studies. Don’t forget the disease triangle  – disease involves plant, pathogen and environment. Effective pathogenicity requires high humidity even when the pathogen is infiltrated directly into the leaf.  Hypothesis HopM1 and AvrE establish an aqueous apoplastic living space for aggressive bacterial multiplication. Water soaking requires high humidity too.

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