Protein phosphatase 2A regulates the nuclear accumulation of the Arabidopsis bZIP protein VIP1 under hypo-osmotic stress

Should I stay or should I go? Trafficking of plant extra-nuclear transcription factors

At the heart of all biological processes lies the control of nuclear gene expression, which is primarily achieved through the action of transcription factors (TFs) that generally contain a nuclear localization signal (NLS) to facilitate their transport into the nucleus. However, some TFs reside in the cytoplasm in a transcriptionally inactive state and only enter the nucleus in response to specific signals, which in plants include biotic or abiotic stresses. These extra-nuclear TFs can be found in the cytosol or associated with various membrane systems, including the endoplasmic reticulum and plasma membrane. They may be integral proteins with transmembrane domains or associate peripherally with the lipid bilayer via acylation or membrane-binding domains. Although over 30 plant TFs, most of them involved in stress responses, have been experimentally shown to reside outside the nucleus, computational predictions suggest that this number is much larger. Understanding how extra-nuclear TFs are trafficked into the nucleus is essential for reconstructing transcriptional regulatory networks that govern major cellular pathways in response to biotic and abiotic signals. Here, we provide a perspective on what is known on plant extranuclear-nuclear TF retention, nuclear trafficking, and the post-translational modifications that ultimately enable them to regulate gene expression upon entering the nucleus.

Calcium signaling-mediated transcriptional reprogramming during abiotic stress response in plants

Calcium (Ca2+) is a second messenger in plants growth and development, as well as in stress responses. The transient elevation in cytosolic Ca2+ concentration have been reported to be involved in plants response to abiotic and biotic stresses. In plants, Ca2+-induced transcriptional changes trigger molecular mechanisms by which plants adapt and respond to environment stresses. The mechanism for transcription regulation by Ca2+ could be either rapid in which Ca2+ signals directly cause the related response through the gene transcript and protein activities, or involved amplification of Ca2+ signals by up-regulation the expression of Ca2+ responsive genes, and then increase the transmission of Ca2+ signals. Ca2+ regulates the expression of genes by directly binding to the transcription factors (TFs), or indirectly through its sensors like calmodulin, calcium-dependent protein kinases (CDPK) and calcineurin B-like protein (CBL). In recent years, significant progress has been made in understanding the role of Ca2+-mediated transcriptional regulation in different processes in plants. In this review, we have provided a comprehensive overview of Ca2+-mediated transcriptional regulation in plants in response to abiotic stresses including nutrition deficiency, temperature stresses (like heat and cold), dehydration stress, osmotic stress, hypoxic, salt stress, acid rain, and heavy metal stress.

The trans-regulatory landscape of gene networks in plants

The transcriptional effector domains of transcription factors play a key role in controlling gene expression; however, their functional nature is poorly understood, hampering our ability to explore this fundamental dimension of gene regulatory networks. To map the trans-regulatory landscape in a complex eukaryote, we systematically characterized the putative transcriptional effector domains of over 400 Arabidopsis thaliana transcription factors for their capacity to modulate transcription. We demonstrate that transcriptional effector activity can be integrated into gene regulatory networks capable of elucidating the functional dynamics underlying gene expression patterns. We further show how our characterized domains can enhance genome engineering efforts and reveal how plant transcriptional activators share regulatory features conserved across distantly related eukaryotes. Our results provide a framework to systematically characterize the regulatory role of transcription factors at a genome-scale in order to understand the transcriptional wiring of biological systems.

"B" Regulatory Subunits of PP2A: Their Roles in Plant Development and Stress Reactions

Protein phosphatase PP2A is an enzyme complex consisting of C (catalytic), A (scaffold) and B (regulatory) subunits. B subunits are a large family of proteins that regulate activity, substrate specificity and subcellular localization of the holoenzyme. Knowledge on the molecular functions of PP2A in plants is less than for protein kinases, but it is rapidly increasing. B subunits are responsible for the large diversity of PP2A functioning. This paper intends to give a survey on their multiple regulatory mechanisms. Firstly, we give a short description on our current knowledge in terms of "B"-mediated regulation of metabolic pathways. Next, we present their subcellular localizations, which extend from the nucleus to the cytosol and membrane compartments. The next sections show how B subunits regulate cellular processes from mitotic division to signal transduction pathways, including hormone signaling, and then the emerging evidence for their regulatory (mostly modulatory) roles in both abiotic and biotic stress responses in plants. Knowledge on these issues should be increased in the near future, since it contributes to a better understanding of how plant cells work, it may have agricultural applications, and it may have new insights into how vascular plants including crops face diverse environmental challenges.

The baseless mutant links protein phosphatase 2A with basal cell identity in the brown alga Ectocarpus

The first mitotic division of the initial cell is a key event in all multicellular organisms and is associated with the establishment of major developmental axes and cell fates. The brown alga Ectocarpus has a haploid-diploid life cycle that involves the development of two multicellular generations: the sporophyte and the gametophyte. Each generation deploys a distinct developmental programme autonomously from an initial cell, the first cell division of which sets up the future body pattern. Here, we show that mutations in the BASELESS (BAS) gene result in multiple cellular defects during the first cell division and subsequent failure to produce basal structures during both generations. BAS encodes a type B″ regulatory subunit of protein phosphatase 2A (PP2A), and transcriptomic analysis identified potential effector genes that may be involved in determining basal cell fate. The bas mutant phenotype is very similar to that observed in distag (dis) mutants, which lack a functional Tubulin-binding co-factor Cd1 (TBCCd1) protein, indicating that TBCCd1 and PP2A are two essential components of the cellular machinery that regulates the first cell division and mediates basal cell fate determination.

GmbZIP152, a Soybean bZIP Transcription Factor, Confers Multiple Biotic and Abiotic Stress Responses in Plant

Soybean is one of the most important food crops in the world. However, with the environmental change in recent years, many environmental factors like drought, salinity, heavy metal, and disease seriously affected the growth and development of soybean, causing substantial economic losses. In this study, we screened a bZIP transcription factor gene, GmbZIP152, which is significantly induced by Sclerotinia sclerotiorum (S. sclerotiorum), phytohormones, salt-, drought-, and heavy metal stresses in soybean. We found that overexpression of GmbZIP152 in Arabidopsis (OE-GmbZIP152) enhances the resistance to S. sclerotiorum and the tolerance of salt, drought, and heavy metal stresses compared to wild-type (WT). The antioxidant enzyme related genes (including AtCAT1, AtSOD, and AtPOD1) and their enzyme activities are induced by S. sclerotiorum, salt, drought, and heavy metal stress in OE-GmbZIP152 compared to WT. Furthermore, we also found that the expression level of biotic- and abiotic-related marker genes (AtLOX6, AtACS6, AtERF1, and AtABI2, etc.) were increased in OE-GmbZIP152 compared to WT under S. sclerotiorum and abiotic stresses. Moreover, we performed a Chromatin immunoprecipitation (ChIP) assay and found that GmbZIP152 could directly bind to promoters of ABA-, JA-, ETH-, and SA-induced biotic- and abiotic-related genes in soybean. Altogether, GmbZIP152 plays an essential role in soybean response to biotic and abiotic stresses.

Prunus persica transcription factor PpNAC56 enhances heat resistance in transgenic tomatoes

Members of the NAC (NAM, ATAF1,2 and CUC2) transcription factor family are involved in numerous processes of plant growth and development and play an important role in the response to abiotic stresses such as salinity, drought and heat, but little research on this topic has been done in peach. In this study, we analyzed the expression patterns of PpNAC56 under abiotic stress and found that PpNAC56 responded to high-temperature stress. To verify the function of PpNAC56, we overexpressed this gene in tomato plants and found that, compared with WT plants, the transgenic tomato plants could accumulate more osmoregulatory substances after high-temperature treatment and thus were more heat resistance. Then, using Y2H, BIFC, and pull-down assays, we found that PpNAC56 could interact with PpMIEL1. In addition, Y1H and dual-luciferase assays verified that PpNAC56 could activate the expression of PpHSP17.4 and PpSnRK2D. The above experimental results demonstrate that PpNAC56 plays an important role in the plant response to heat stress.

SWO1 modulates cell wall integrity under salt stress by interacting with importin ɑ in Arabidopsis

Maintenance of cell wall integrity is of great importance not only for plant growth and development, but also for the adaptation of plants to adverse environments. However, how the cell wall integrity is modulated under salt stress is still poorly understood. Here, we report that a nuclear-localized Agenet domain-containing protein SWO1 (SWOLLEN 1) is required for the maintenance of cell wall integrity in Arabidopsis under salt stress. Mutation in SWO1 gene results in swollen root tips, disordered root cell morphology, and root elongation inhibition under salt stress. The swo1 mutant accumulates less cellulose and pectin but more lignin under high salinity. RNA-seq and ChIP-seq assays reveal that SWO1 binds to the promoter of several cell wall-related genes and regulates their expression under saline conditions. Further study indicates that SWO1 interacts with importin ɑ IMPA1 and IMPA2, which are required for the import of nuclear-localized proteins. The impa1 impa2 double mutant also exhibits root growth inhibition under salt stress and mutations of these two genes aggravate the salt-hypersensitive phenotype of the swo1 mutant. Taken together, our data suggest that SWO1 functions together with importin ɑ to regulate the expression of cell wall-related genes, which enables plants to maintain cell wall integrity under high salinity.

NDR/LATS-family protein kinase genes are indispensable for embryogenesis in Arabidopsis

NDR/LATS‐family protein kinases are conserved among eukaryotes. These protein kinases in yeast and animals phosphorylate specific targets and regulate the cell cycle. Arabidopsis thaliana has eight NDR/LATS‐family protein kinase genes (NDR1‐8), of which NDR2, NDR4, and NDR5 are involved in regulating pollen development. However, the functions of the other NDR/LATS‐family protein kinase genes in plants are unclear. Here, we show that three putative phosphorylation sites of an Arabidopsis basic leucine zipper transcription factor, VIP1, correspond to NDR/LATS‐family protein kinase phosphorylation motifs and that two of these three sites are phosphorylated by NDR2, NDR3, or NDR8 in vitro. Expression of NDR1‐8 was detected in various tissues. An NDR4 NDR6 NDR7 NDR8 quadruple mutation caused embryonic lethality These results suggest that different NDR/LATS‐family protein kinases in plants have distinct physiological roles.

Arabidopsis bZIP18 and bZIP52 Accumulate in Nuclei Following Heat Stress where They Regulate the Expression of a Similar Set of Genes

Heat stress (HS) is a major abiotic stress that negatively impacts crop yields across the globe. Plants respond to elevated temperatures by changing gene expression, mediated by transcription factors (TFs) functioning to enhance HS tolerance. The involvement of Group I bZIP TFs in the heat stress response (HSR) is not known. In this study, bZIP18 and bZIP52 were investigated for their possible role in the HSR. Localization experiments revealed their nuclear accumulation following heat stress, which was found to be triggered by dephosphorylation. Both TFs were found to possess two motifs containing serine residues that are candidates for phosphorylation. These motifs are recognized by 14–3–3 proteins, and bZIP18 and bZIP52 were found to bind 14–3–3 ε, the interaction of which sequesters them to the cytoplasm. Mutation of both residues abolished 14–3–3 ε interaction and led to a strict nuclear localization for both TFs. RNA-seq analysis revealed coordinated downregulation of several metabolic pathways including energy metabolism and translation, and upregulation of numerous lncRNAs in particular. These results support the idea that bZIP18 and bZIP52 are sequestered to the cytoplasm under control conditions, and that heat stress leads to their re-localization to nuclei, where they jointly regulate gene expression.

Genomic Analysis of Soybean PP2A-B ' ' Family and Its Effects on Drought and Salt Tolerance

Abiotic stresses induce the accumulation of reactive oxygen species (ROS) and significantly affect plant growth. Protein phosphatase 2A (PP2A) plays an important role in controlling intracellular and extracellular ROS signals. However, the interaction between PP2A, ROS, and stress tolerance remains largely unclear. In this study, we found that the B ' ' subunit of PP2A (PP2A-B ' ' ) can be significantly induced and was analyzed using drought- and salt-induced soybean transcriptome data. Eighty-three soybean PP2A-B ' ' genes were identified from the soybean genome via homologous sequence alignment, which was distributed across 20 soybean chromosomes. Among soybean PP2A-B ' ' family genes, 26 GmPP2A-B ' ' members were found to be responsive to drought and salt stresses in soybean transcriptome data. Quantitative PCR (qPCR) analysis demonstrated that GmPP2A-B ' ' 71 had the highest expression levels under salt and drought stresses. Functional analysis demonstrated that overexpression of GmPP2A-B ' ' 71 in soybeans can improve plant tolerance to drought and salt stresses; however, the interference of GmPP2A-B ' ' 71 in soybean increased the sensibility to drought and salt stresses. Further analysis demonstrated that overexpression of GmPP2A-B ' ' 71 in soybean could enhance the expression levels of stress-responsive genes, particularly genes associated with ROS elimination. These results indicate that PP2A-B ' ' can promote plant stress tolerance by regulating the ROS signaling, which will contribute to improving the drought resistance of crops.

The B″-family subunits of protein phosphatase 2A are necessary for in-vitro dephosphorylation of the Arabidopsis mechanosensory transcription factor VIP1

Protein phosphatase 2A (PP2A) B″-family subunits have Ca²⁺-binding EF-hand motifs and can bind PP2A substrates. Arabidopsis thaliana PP2A B″-family subunits are encoded by six genes, and bind a transcription factor, VIP1. VIP1 is dephosphorylated and nuclear-localized by hypo-osmotic stress. However, whether PP2A B″-family subunits mediate the VIP1 dephosphorylation is unclear. Here, we show by yeast two-hybrid and in vitro pull down assays that Arabidopsis PP2A B″-family subunits bind Arabidopsis PP2A A (scaffold) subunits. We also show that VIP1 dephosphorylation in vitro can be induced by a PP2A B″-family subunit.

Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat

AIM

To establish a gene co-expression network for identifying principal modules and hub genes that are associated with drought resistance mechanisms, analyzing their mechanisms, and exploring candidate genes.

METHODS AND FINDINGS

42 data sets including PRJNA380841 and PRJNA369686 were used to construct the co-expression network through weighted gene co-expression network analysis (WGCNA). A total of 1,896,897,901 (284.30 Gb) clean reads and 35,021 differentially expressed genes (DEGs) were obtained from 42 samples. Functional enrichment analysis indicated that photosynthesis, DNA replication, glycolysis/gluconeogenesis, starch and sucrose metabolism, arginine and proline metabolism, and cell cycle were significantly influenced by drought stress. Furthermore, the DEGs with similar expression patterns, detected by K-means clustering, were grouped into 29 clusters. Genes involved in the modules, such as dark turquoise, yellow, and brown, were found to be appreciably linked with drought resistance. Twelve central, greatly correlated genes in stage-specific modules were subsequently confirmed and validated at the transcription levels, including TraesCS7D01G417600.1 (PP2C), TraesCS5B01G565300.1 (ERF), TraesCS4A01G068200.1 (HSP), TraesCS2D01G033200.1 (HSP90), TraesCS6B01G425300.1 (RBD), TraesCS7A01G499200.1 (P450), TraesCS4A01G118400.1 (MYB), TraesCS2B01G415500.1 (STK), TraesCS1A01G129300.1 (MYB), TraesCS2D01G326900.1 (ALDH), TraesCS3D01G227400.1 (WRKY), and TraesCS3B01G144800.1 (GT).

CONCLUSIONS

Analyzing the response of wheat to drought stress during different growth stages, we have detected three modules and 12 hub genes that are associated with drought resistance mechanisms, and five of those genes are newly identified for drought resistance. The references provided by these modules will promote the understanding of the drought-resistance mechanism. In addition, the candidate genes can be used as a basis of transgenic or molecular marker-assisted selection for improving the drought resistance and increasing the yields of wheat.

Agrobacterium tumefaciens: A Bacterium Primed for Synthetic Biology

Agrobacterium tumefaciens is an important tool in plant biotechnology due to its natural ability to transfer DNA into the genomes of host plants. Genetic manipulations of A. tumefaciens have yielded considerable advances in increasing transformational efficiency in a number of plant species and cultivars. Moreover, there is overwhelming evidence that modulating the expression of various mediators of A. tumefaciens virulence can lead to more successful plant transformation; thus, the application of synthetic biology to enable targeted engineering of the bacterium may enable new opportunities for advancing plant biotechnology. In this review, we highlight engineering targets in both A. tumefaciens and plant hosts that could be exploited more effectively through precision genetic control to generate high-quality transformation events in a wider range of host plants. We then further discuss the current state of A. tumefaciens and plant engineering with regard to plant transformation and describe how future work may incorporate a rigorous synthetic biology approach to tailor strains of A. tumefaciens used in plant transformation.

VIP1, a bZIP protein, interacts with the catalytic subunit of protein phosphatase 2A in Arabidopsis thaliana

VirE2-INTERACTING PROTEIN1 (VIP1) is a basic leucine zipper protein in Arabidopsis thaliana. VIP1 changes its subcellular localization from the cytoplasm to the nucleus when cells are exposed to mechanical or hypo-osmotic stress. The nuclear localization of VIP1 is inhibited either by inhibitors of calcium signaling or by inhibitors of protein phosphatases 1, 2A and 4 (PP1, PP2A and PP4, respectively). VIP1 binds to the PP2A B"-family subunits, which have calcium-binding EF-hand motifs and which act as the regulatory, substrate-recruiting B subunit of PP2A. The VIP1 de-phosphorylation can therefore be mediated by PP2A. However, details of the PP2A-mediated de-phosphorylation of VIP1 are unclear. Here, with yeast two-hybrid assays and in-vitro pull-down assays, we show that VIP1 does not interact with the scaffolding A subunit of PP2A, but that VIP1 does interact with the catalytic C subunits. Our data raise the possibility that not only the B"-family B subunit of PP2A but also its C subunit contributes to the PP2A-mediated de-phosphorylation of VIP1.