Jyan-Chyun Jang

Processing bodies (PBs) and stress granules (SGs) are membrane-less cellular compartments consisting of ribonucleoprotein complexes. Whereas PBs are more ubiquitous, SGs are assembled mainly in response to stress. PBs and SGs are known to physically interact and molecules exchange between the two have been documented in mammals. However, the molecular mechanisms underpinning these processes are virtually unknown in plants. We have reported recently that tandem CCCH zinc finger 1 (TZF1) protein can recruit MAPK signaling components to SGs. Here we have found that TZF1-MPK3/6-MKK4/5 form a protein-protein interacting network in SGs. The mRNA decapping factor 1 (DCP1) is a core component of PBs. MAPK signaling mediated phosphorylation triggers a rapid reduction of DCP1 partition into PBs, concomitantly associated with an increase of DCP1 assembly into SGs. Furthermore, we have found that plant SG marker protein UBP1b (oligouridylate binding protein 1b) plays a role in maintaining DCP1 in PBs by suppressing the accumulation of MAPK signaling components. Together, we propose that MAPK signaling and UBP1b mediate the dynamics of PBs and SGs in plant cells.

Tandem CCCH zinc finger (TZF) proteins play diverse roles in plant growth and stress response. Although as many as 11 TZF proteins have been identified in Arabidopsis, little is known about the mechanism by which TZF proteins select and regulate the target mRNAs. Here, we report that Arabidopsis TZF1 is a bona-fide stress granule protein. Ectopic expression of TZF1 (TZF1 OE), but not an mRNA binding-defective mutant (TZF1^H186Y OE), enhances salt stress tolerance in Arabidopsis. RNA-seq analyses of NaCl-treated plants revealed that the down-regulated genes in TZF1 OE plants are enriched for functions in salt and oxidative stress responses. Because many of these down-regulated mRNAs contain AU- and/or U-rich elements (AREs and/or UREs) in their 3’-UTRs, we hypothesized that TZF1—ARE/URE interaction might contribute to the observed gene expression changes. Results from RNA immunoprecipitation-quantitative PCR analysis, gel-shift, and mRNA half-life assays indicate that TZF1 binds and triggers degradation of the autoinhibited Ca²⁺-ATPase 11 (ACA11) mRNA, which encodes a tonoplast-localized calcium pump that extrudes calcium and dampens signal transduction pathways necessary for salt stress tolerance. Furthermore, this salt stress-tolerance phenotype was recapitulated in aca11 null mutants. Collectively, our findings demonstrate that TZF1 binds and initiates degradation of specific mRNAs to enhance salt stress tolerance.

The Arabidopsis tandem CCCH zinc finger 1 (TZF1) is an RNA-binding protein that plays a crucial role in plant growth and stress response. TZF1 can localize to ribonucleoprotein (RNP) granules in response to various abiotic stresses. However, very little is known about the composition, function, and assembly mechanism of plant RNP granules. In this report, we show that TZF1 contains two intrinsically disordered regions (IDRs) necessary for its localization to stress granules (SGs), a subclass of RNP granules. TZF1 recruits mitogen-activated protein kinase (MAPK) signaling components and an E3 ubiquitin ligase KEEP-ON-GOING (KEG) to SGs. TZF1 is phosphorylated by MPKs and ubiquitinated by KEG. The phosphorylation sites of TZF1 were mapped by mass spectrometry. Mutant studies revealed that phosphorylation and ubiquitination of specific residues played differential roles in enhancing or reducing TZF1 SG assembly and protein-protein interaction with mitogen-activated kinase kinase 5 (MKK5) in SGs. TZF1 is extremely unstable, and its accumulation can be enhanced by proteosome inhibitor MG132. We showed that TZF1 was ubiquitinated in vivo and in vitro by KEG and TZF1 accumulated at a much lower level in gain-of-function mutant keg-4 , compared to the WT. Ubiquitination appeared to play a positive role in TZF1 SG assembly, because either single or higher order mutations caused reduced number of SGs per cell, while enhanced the coalescence of small SGs into a large nucleus-like SG encompassing the nucleus. Together, our results demonstrate that the assembly of TZF1 SGs is distinctively regulated by ubiquitination and phosphorylation.

Tandem CCCH zinc finger (TZF) proteins play diverse roles in plant growth and stress response. Although as many as 11 TZF proteins have been identified in Arabidopsis , little is known about the mechanism by which TZF proteins select and regulate the target mRNAs. Here, we report that Arabidopsis TZF1 is a bona-fide stress granule protein. Ectopic expression of TZF1 ( TZF1 OE ), but not an mRNA binding-defective mutant ( TZF1 ^H186Y OE ), enhances salt stress tolerance in Arabidopsis . RNA-seq analyses of NaCl-treated plants revealed that the down-regulated genes in TZF1 OE plants are enriched for functions in salt and oxidative stress responses. Because many of these down-regulated mRNAs contain AU- and/or U-rich elements (AREs and/or UREs) in their 3’-UTRs, we hypothesized that TZF1—ARE/URE interaction might contribute to the observed gene expression changes. Results from RNA immunoprecipitation-quantitative PCR analysis, gel-shift, and mRNA half-life assays indicate that TZF1 binds and triggers degradation of the autoinhibited Ca ²⁺ -ATPase 11 ( ACA11 ) mRNA, encoding a tonoplast-localized calcium pump that extrudes calcium and dampens the signal transduction pathways necessary for salt stress tolerance. Furthermore, this salt stress-tolerance phenotype was recapitulated in aca11 null mutants. Remarkably, a set of positive regulators for salt stress tolerance was upregulated in TZF1 OE plants. These include Na ⁺ /H ⁺ Exchanger ( NHX ) family members known to contribute to Na ⁺ homeostasis and salinity stress tolerance. Collectively, we present a model in which TZF1 targets ACA11 and ACA4 directly, and repressors of NHXs and other negative regulators indirectly for mRNA degradation to enhance plant salt stress tolerance.

Leaves are essential plant organs with numerous variations in shape and size. The leaf size is generally smaller in plants that thrive in areas of higher elevation and lower annual mean temperature. The Qinghai–Tibetan Plateau is situated at an altitude of >4000 m with relatively low annual average temperatures. Most plant species found on the Qinghai–Tibetan Plateau have small leaves, with Rheum tanguticum Maxim. ex Balf. being an exception. Here, we show that the large leaves of R. tanguticum with a unique three-dimensional (3D) shape are potentially an ideal solution for thermoregulation with little energy consumption. With the increase in age, the shape of R. tanguticum leaves changed from a small oval plane to a large palmatipartite 3D shape. Therefore, R. tanguticum is a highly heteroblastic species. The leaf shape change during the transition from the juvenile to the adult phase of the development in R. tanguticum is a striking example of the manifestation of plant phenotypic plasticity. The temperature variation in different parts of the leaf was a distinct character of leaves of over-5-year-old plants. The temperature of single-plane leaves under strong solar radiation could accumulate heat rapidly and resulted in temperatures much higher than the ambient temperature. However, leaves of over-5-year-old plants could lower leaf temperature by avoiding direct exposure to solar radiation and promoting local airflow to prevent serious tissue damage by sunburn. Furthermore, the net photosynthesis rate was correlated with the heterogeneity of the leaf surface temperature. Our results demonstrate that the robust 3D shape of the leaf is a strategy that R. tanguticum has developed evolutionarily to adapt to the strong solar radiation and low temperature on the Qinghai–Tibetan Plateau.

RNA granules, such as stress granules and processing bodies, can balance the storage, degradation, and translation of mRNAs in diverse eukaryotic organisms. The sessile nature of plants demands highly versatile strategies to respond to environmental fluctuations. In this review, we discuss recent findings of the dynamics and functions of these RNA granules in plants undergoing developmental reprogramming or responding to environmental stresses. Special foci include the dynamic assembly, disassembly, and regulatory roles of these RNA granules in determining the fate of mRNAs.

Ubiquitous CCCH nucleic acid-binding motif is found in a wide-variety of organisms. CCCH genes are involved in plant developmental processes and biotic and abiotic stress responses. Brassica rapa is a vital economic crop and classical model plant of polyploidy evolution, but the functions of CCCH genes in B. rapa are unclear. In this study, 103 CCCH genes in B. rapa were identified. A comparative analysis of the chromosomal position, gene structure, domain organization and duplication event between B. rapa and Arabidopsis thaliana were performed. Results showed that CCCH genes could be divided into 18 subfamilies, and segmental duplication might mainly contribute to this family expansion. C-X7/8-C-X5-C3-H was the most commonly found motif, but some novel CCCH motifs were also found, along with some loses of typical CCCH motifs widespread in other plant species. The multifarious gene structures and domain organizations implicated functional diversity of CCCH genes in B. rapa. Evidence also suggested functional redundancy in at least one subfamily due to high conservation between members. Finally, the expression profiles of subfamily-IX genes indicated that they are likely involved in various stress responses. This study provides the first genome-wide characterization of the CCCH genes in B. rapa. The results suggest that B. rapa CCCH genes are likely functionally divergent, but mostly involved in plant development and stress response. These results are expected to facilitate future functional characterization of this potential RNA-binding protein family in Brassica crops.