Session 3
Authors: Chua Nam-Hai , Pasion Erstelle , Magen Sahar , Tolessa Tamene , Tan Qiao Wen , Josse Max 
Published: July 2023

Phase separation and mobile noncoding RNA regulate leaf senescence

Nitrogen is an essential macronutrient that is absorbed by roots and stored in leaves, mainly as ribulose-1,5-bisphosphate carboxylase/oxygenase. To adapt to nitrogen deficiency (-N), leaf senescence facilitates nitrogen redistribution. As the key transcription factor of Arabidopsis thaliana senescence, ORESARA1 (ORE1) is required for nitrogen deficiency (-N) induced senescence. Here, two essential observations were made. First, we found that Arabidopsis MED19a associates with ORE1 to activate -N senescence-responsive genes. Disordered MED19a forms inducible nuclear condensates under -N that is regulated by decreasing MED19a lysine acetylation. MED19a carboxyl terminus (cMED19a) harbors a mixed-charged intrinsically disordered region (MC-IDR) required for ORE1 interaction and liquid-liquid phase separation (LLPS). Second, -N signals, which are initially perceived by roots, are subsequently propagated to shoots to trigger senescence; however, the mechanism of -N signal propagation remains underexplored. We found that ELF18-INDUCED LONG NONCODING RNA 1 (ELENA1) is -N inducible and attenuates -N induced senescence in Arabidopsis. Analysis of plants expressing ELENA1 promoter β-glucuronidase fusion gene showed that ELENA1 is transcribed specifically in roots under -N. Reciprocal grafting of WT and elena1 demonstrated that ELENA1 functions systemically. ELENA1 dissociates the MEDIATOR SUBUNIT 19a-ORESARA1 transcriptional complex thereby calibrating senescence progression. Our observations establish the systemic regulation of leaf senescence by a root-derived long noncoding RNA under -N in Arabidopsis.

Unraveling the genetics underlying micronutrient signatures of diversity panel present in brown rice through genome-ionome linkages

Rice (Oryza sativa) is an important staple crop to address the Hidden Hunger problem. The brown rice is known to be nutritious due to elevated mineral composition. The genetics underlying brown rice ionome remains largely unexplored. Hence, we conducted a comprehensive study to dissect the genetic architecture of the brown rice ionome. We used genome-wide association studies (GWAS), gene set analysis, and targeted association analysis for 12 micronutrients in the brown rice grains. A diverse panel of 300 resequenced indica accessions, with more than 1.02 million single nucleotide polymorphisms, was used. We identified 109 candidate genes with 5-20% phenotypic variation explained (PVE) for the 12 micronutrients with epistatic interactions for multiple micronutrients. Pooling all candidate genes per micronutrient exhibited PVE values ranging from 11% to almost 40%. The key donor lines with larger concentrations for most of the micronutrients possessed superior alleles, which were absent in the breeding lines. Through gene regulatory networks we identified enriched functional pathways for central regulators that were detected as key candidate genes through GWAS. This study provided important insights on the ionome variations in rice, on the genetic basis of the genome-ionome relationships, and on the molecular mechanisms underlying micronutrient signatures.

Raffinose as a novel inducer of autophagy in plants

Autophagy, an intracellular degradation and recycling process, is gaining attention as a stress-coping mechanism in eukaryotes. It is induced by many nutrient-deprivation conditions and biotic and abiotic stresses in plants. Over-expression of autophagy-related genes in several plant species increased plant size, yield, and stress resistance. Yet, regulatory restrictions on transgenic plants hinder the direct modulation of autophagy in crops, and the constitutive induction of autophagy might prove unuseful in all environmental conditions. Thus, other means of modulating autophagy are needed. Previous works from plant and animal systems demonstrated the possible role of regulatory sugars in autophagy stimulation. Our research aims to find a natural sugar that activates autophagy in plants by spraying. We identified the trisaccharide raffinose as an autophagy inducer in plants. We demonstrate that raffinose treatment increased the performance of several crop species, both monocot and eudicot, and seed yield in an autophagy-dependent mannerin growth room and field conditions. The data gained in this project will help elucidate how regulatory sugars influence autophagy in plants. Moreover, it will serve as the basis for developing raffinose, and possibly other autophagy regulators, as agrochemicals to improve crop plant growth and yield.

Myrtaceae tree species encodes for a potential novel class of resistance genes

Many species of Myrtaceae, an economically and ecologically significant plant family in Australia are threatened by myrtle rust infection caused by Austropuccinia psidii. We conducted a comprehensive analysis of R-genes that encode for nucleotide-binding sites (NBS) using long-read sequences of 28 species to investigate the genetic basis of disease resistance. We predicted 1.04 million gene models encoding 47.7k NBS and leucine-rich repeat (LRR) domains. We detected 260 unique domains with diverse frequencies of integration into NBS-LRR genes. A single Jacalin domain accounted for 43.1% of the total integration frequency. Tol/interleukin-1 (TIR), which encodes for NBS but lacks LRR, was highly expanded with 1-10 copies of Jacalin (J) in its C-terminal (TNJ). TNJ formed a monophyletic clade nested within the TN that encodes for LRR (TNL) clades. Important nucleotide-binding motifs and functional amino-acid residues were conserved in the TNJ. Similar to what has been observed in LRR domains elsewhere, hyper-variable and positively selected sites were found clustered in the Jacalin region of TNJ. Thus, Jacalin may be a functional analogue of LRR in terms of pathogen molecule recognition. Our findings reveal that different tree families could evolve with different pathogen recognition specificity, and clade-specific R-gene organization might contribute to specific niche adaptation in distinct plant families.

Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses

The response of plants to cross-stress is poorly understood and is reported to be non-additive with respect to its single stress response. Plants are expected to be exposed to multiple stress conditions in higher frequency and of higher intensity amidst the outlook of climate change. In this study, we explored the response of Marchantia polymorpha, an early diverging land plant to 7 abiotic stresses (cold, darkness, heat, light, mannitol, nitrogen deficiency and salt) and 19 pairwise combinations through the lens of differential expression, inferred regulatory relationships, conservation of regulation with respect to Arabidopsis and the relationship between gene expression values (log2 fold-change) during single and cross-stress using linear regression. The observation of dominance, non-additivity and novel responses in cross-stress was congruent with what has been described in the literature. Regulatory relationships inferred were often stress-specific and Arabidopsis TF orthologs were responsive in a wider range of stresses in contrast to stress-specific Marchantia TFs. Remarkably, we discovered that gene expression values of cross-stress datasets could be accurately predicted with the values of single stress through linear regression, and the predictive power of single stress corresponded to its dominance in relation to other stresses.

Detecting cellular auxin dynamics in living plants – microbial auxin sensors domains break the ice

This talk will not be available to watch on demand.

The auxin research field is highly advanced with functional models of cellular dynamics of IAA impacting nearly all aspects of plant physiology and development. However, these are largely based on either destructive, lower-resolution direct measurements (e.g. GC-MS) or indirect measurements in vivo (e.g. DR5, DII-Venus). Hence, our goal is to engineer direct biosensors for auxin based on FRET (Förster Resonance Energy Transfer), analogous to other ratiometric biosensors for plant hormones. We engineered IAA Genetically-encoded Optical FRET biosensors (IAAGO1/IAAGO2), to track auxin dynamics directly, in real-time and with subcellular resolution in a minimally invasive manner. IAAGO1 is derived from a prokaryotic biosensor protein and had IAA affinity of  1.5µM, that we later optimised to a present version with higher affinity (KdIAA  400nM). IAAGO1 responds to auxin with high signal-to-noise ratio in E. coli, yeast, in planta and in vitro. IAAGO2 is derived from an initial biosensor protein that we engineered for very high affinity (KdIAA  10nM) for auxin, comparable to auxin physiological range. Already IAAGO2s have revealed novel auxin dynamics in the cell nuclei of growing Arabidopsis organs and ongoing optimisation efforts will establish IAAGO2 utility for illuminating the many biological phenomena where cellular auxin dynamics are thought to be determinative.