Wong et al., 2019 PNAS

The mechanisms plants use to detect and signal abiotic stress are not well understood but have major implications for plant productivity during periods of drought and other environmental stresses. Clade A Protein Phosphatases 2Cs (PP2Cs) are part of the core signaling pathway of the stress hormone Abscisic Acid which regulates many plant stress responses.  In previous research, the Verslues laboratory noted that the Clade A PP2C Highly ABA-Induced 1 (HAI1) has especially prominent effects on drought phenotypes such as growth and proline accumulation (Bhaskara et al., 2012).  To investigate how HAI1 affects drought response, phosphoproteomic analysis of the hai1-2 mutant was conducted for plants under unstressed conditions or after low water potential (drought) treatment (Wong et al., 2019 PNAS).  This identified more than 100 phosphopeptides of increased abundance in hai1-2, indicating that phosphorylation status of these sites could be regulated by HAI1 directly of via HAI1-regulated kinases.  Further experiments on At-Hook Like 10, a nuclear localized DNA-binding protein of unclear function, demonstrated that it could be directly dephosphorylated by HAI1.  The S314 phosphorylation site identified in our proteomics analysis was crucial for AHL10 regulation of growth and gene expression during low water potential stress and was also required for AHL10 complexes to form nuclear foci. By identifying HAI1-affected phosphoproteins and functionally important AHL10 phosphorylation site, these results elucidate HAI1 and AHL10 function and also demonstrate a mechanism plants use to balance maximal growth versus robust response to environmental stress. 

Chen et al, PNAS 2018

          Plants are capable of transforming sunlight energy to chemical energy stored in carbohydrates. The presence or absence of light also serves as important environmental cues for plants to deploy appropriate developmental programs for coping with the environment. Photomorphogenesis is an essential developmental process transforming young plant seedlings into the vegetative phase with photosynthetic activities. Despite the abundant knowledge of transcriptional and post-translational regulation in photomorphogenesis, translational control by light signals is much less discussed. We previously showed that light activates the translation of thousands of mRNAs in de-etiolating seedlings. What remains to be revealed is the underlying molecular mechanism responsible for the massive translation triggered by light signals in de-etiolating Arabidopsis seedlings.  

        We showed that light-enhanced translation is orchestrated by a light perception and signaling pathway composed of photoreceptors, CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1), the phytohormone auxin, target of rapamycin (TOR) and ribosomal protein S6 (RPS6). In de-etiolating Arabidopsis seedlings, photoreceptors including phytochrome A and cryptochromes perceive far-red and blue light to inactivate the negative regulator COP1, which leads to activation of the auxin pathway for TOR-dependent phosphorylation of RPS6. Arabidopsis mutants defective in TOR, RPS6A or RPS6B exhibited delayed cotyledon opening, a characteristic of the de-etiolating process to ensure timely vegetative development of a young seedling. This study provides a mechanistic view of light-triggered translational enhancement in de-etiolating Arabidopsis. This sophisticated regulation also functions to ensure that young seedlings have strict skotomorphogenic development in the dark and a timely switch to photomorphogenic development. (Chen et al, PNAS 2018)


2019/2/13 Get to Know IPMB Activity

Date: February 13, 2019

Venue: Room A134, A134, Agricultural Technology Building, Academia Sinica

Target Audience: Undergraduate students

(This is a Chinese-speaking activity.)

Online Registration (Deadline: 5:00 PM, January 31, 2019)

Liu et al., 2018, Plant Physiology

Phosphatidylcholine (PC) is the major phospholipid class in most eukaryotes. However, it remained unknown whether PC biosynthesis is essential for plants. A research group led by Dr. Yuki Nakamura showed a methyltransferase trio, PMT1, 2, and 3, essential for PC biosynthesis in Arabidopsis. The triple mutant has no ability to synthesize PC and shows severe seedling growth, albeit they can germinate. Thus, an essential role of PC biosynthesis in postembryonic growth is now revealed in plants 170 years after the first discovery of PC in egg yolk.

Hsieh et al., 2018, RNA Biology

Fig. 1 Allotopic expression of nad7 rescues the Arabidopsis mutant slow growth3 (slo3).


Plant pentatricopeptide repeat (PPR) proteins are mostly involved in chloroplast or mitochondrial RNA metabolism. However, direct evidence that correction of the molecular defects in the organelles can restore the plant phenotypes has yet to be demonstrated in a ppr mutant. Dr. Ming-Hsiun Hsieh’s laboratory has used slow growth3 (slo3) as an example to demonstrate that transformation of correctly spliced nad7 into the nuclear genome and targeting the Nad7 subunit into mitochondria can restore complex I activity and plant phenotypes in the mutant (Fig. 1). These results provide direct evidence that the strong growth and developmental phenotypes of the slo3 mutant are caused by defects in mitochondrial nad7.

Wang, Yu et al., 2018

Erh-Min Lai group previously developed a highly efficient Agrobacterium-mediated transient expression system, named AGROBEST, for Arabidopsis seedlings (1) (Wu et al., 2014). The group has further explored the rationales of the enhancement and has recently reported in Scientific Reports (2) (Wang, Yu et al., 2018). Maintaining a stable acidic environment suppresses the immune response of Arabidopsis seedlings. As a result, the seedlings become more susceptible to Agrobacterium-mediated transformation and have better expression of foreign genes carried by the T-DNA.  The authors further illustrate that the stable acidic pH inhibits the calcium uptake induced by pathogen-associated molecular patterns (PAMPs) which could be the cause of suppression in immune response.  The authors hope that this study can help to improve transformation efficiency, especially for plant species recalcitrant to genetic engineering or with limited knowledge of genetic background.

Hou et al., 2018, PNAS

Figure: Ratio distributions of gene expression in each trisomic and ploidy compared to diploids.

The sequencing reads from RNA-Seq were averaged for the biological replicates. For each expressed gene, a ratio of the averaged read counts in the respective experimental (trisomic or ploidy) genotype was made over the read counts in the diploid control. These ratios were plotted in bins of 0.05. The X axis notes the value for each bin and the Y axis notes the number of genes per bin. For the five trisomics, genes were partitioned into those encoded on the varied chromosome (cis) versus those encoded on the remainder of the genome that was not varied in dosage (trans). A ratio of 1.00 represents no change in the experimental genotype versus the diploid. A ratio of 1.50 represents a gene dosage effect in cis whereas 1.00 represents dosage compensation. A ratio of 0.67 represents the inverse ratio of gene expression in trans. These ratio values are demarcated with labeled vertical lines. The triploid and tetraploid ploidy series were analyzed in the same manner for all expressed genes. The vertical demarcations in this case correspond to the respective direct or inverse relationship of the ploidy comparison. The tetraploid/triploid comparison was generated by producing the respective ratios and plotting the distribution. Each comparison is labeled in the respective panel.


Changes in dosage of part of the genome (aneuploidy) have long been known to produce more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To study the basis of these differences, we examined, global gene expression in mature leaf tissue for all five trisomics and in diploids, triploids and tetraploids of Arabidopsis thaliana. The trisomics produced a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was investigated in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is usually mechanistically unrelated to DNA methylation. Independent inspection of gene functional classes demonstrated that ribosomal, proteasomal and gene body methylated genes were less modulated compared to all classes of genes whereas genes encoding transcription factors, signal transduction components and organelle-targeted proteins were more tightly inversely affected. Comparing transcription factors and their targets in the trisomics and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Re-analysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa and indicated that these responses reflect normal gene regulatory processes.

Grillet et al., 2018, Nature Plants

Iron is an essential mineral nutrient which severely affects the growth, yield, and nutritional quality of plants if not supplied in sufficient quantities. Wolfgang Schmidt’s group discovered a novel family of peptides in plants referred to as IRON MAN (IMA), and show that they are a sine qua non for the uptake of iron the soil. Silencing of all eight IMA genes in Arabidopsis by CRISPR-Cas9 genome editing resulted in very small, extremely chlorotic plants that died without drastic iron supplementation. IMAs are present in the genomes of all flowering plants but are missing in ferns, algae or fungi, suggesting that IMA emerged at an early stage in the evolution of land plants. Reciprocal grafting of octuple ima mutants with wild-type plants showed that IMA1 peptides in shoots positively regulate iron uptake in roots, suggesting that IMAs are the long sought-after shoot-borne signal that communicates the iron status of the leaves to tune iron uptake by roots. The discovery of IRON MAN opens a novel route of generating iron-enriched plants that may help to combat iron deficiency-induced anaemia, one of the largest nutritional disorder in humans.