Plants are the source of our food, medicine, construction materials, and the foundation of ecosystems. How can we improve the productivity and resilience of plants? What knowledge, technologies, and tools do we need to generate? These are the long-term questions Zhiyong Wang's lab aim to answer in their research.
Plant growth and survival depend on cellular signaling mechanisms through which plant cells monitor and respond to hormonal signals, environmental cues, and internal nutrient status. Brassinosteroid (BR) is a major growth-promoting hormone that effects on plant height, size, and biomass accumulation.
Plant growth and development are also highly sensitive to environmental signals such as light/dark, temperature, and pathogens. Of course, plant growth depends on nutrients including nitrogen and sugars (product of photosynthesis), and nutrient-sensing mechanisms, such as the Target of Rapamycin (TOR) kinase or O-glycosyltransferases (SPINDLY and SECRET AGENT), are essential for viability.
Zhiyong Wang's research dissects the molecular mechanisms underlying growth responses to these internal and external factors, which have major impacts on plant growth and resilience. To achieve a comprehensive and mechanistic understanding of the growth regulatory system, his lab uses broad research approaches and technologies, including genomics, proteomics, chemical proteomics, microscopy, computation, and structural biology.
Accomplishments
The Wang Lab's research has established the framework of molecular networks that explain how nutritional, hormonal, and environmental signals coordinate the cellular decisions of growth, immunity, and acclimation. Most of the former postdocs and students who made these important discoveries are now leading their own labs in academic institutions.
Among the major achievements of our research, Zhiyong Wang's team has illustrated:
The full brassinosteroid (BR) signaling pathway from the receptor kinase BRI1 to nuclear transcription factor BZR1 and its thousands of target genes.
The growth co-regulation by key growth hormones (BR, auxin, gibberellin) and environmental signals (light and temperature) through direct interactions among their responsive transcription factors, a signal integration mechanism named BAP/D module
The spatiotemporal actions of BR in patterning growth and development in the shoot and root tips.
The mechanisms of crosstalk and component-sharing between BR/BRI1 and other receptor kinase pathways that regulate stomata development and immunity.
The expansive BR-response phosphorylation network controlled by the BIN2/GSK3 kinase.
The genetic variations in the BR-response cis-elements contribute to traits in maize.
The expansive nutrient-signaling networks of protein posttranslational modifications by O-linked β-N-acetylglucosamine (O-GlcNAc) and O-fucose.
The significant overlaps between the BR-regulated phosphorylation network and the nutrient-dependent O-glycosylation networks.
Ongoing Work:
Building upon a large amount of solid data and converging discoveries while taking advantage of the in-house mass spectrometry facility/technologies, our current research continues to make exciting progress toward answering important scientific questions. These include:
How does BR-dependent phosphorylation regulate membrane trafficking, an essential aspect of cell growth?
How do the BR-signaling proteins regulate cytokinesis in plants?
How do cells maintain cell wall integrity during hormone-induced cell expansion?
How do O-GlcNAcylation and O-fucosylation mediate sugar regulation of protein functions and cellular/developmental/physiological processes?
How do BR and sugar signaling, through phosphorylation and O-glycosylation, respectively, co-regulate metabolism and growth?
How do phosphorylation and O-glycosylation crosstalk on common target proteins?
These projects are led by individual postdocs and graduate students, who collaborate and support each other, under my guidance. Together, we are advance a systems-level mechanistic understanding of plant growth and acclimation, and we identify targets and strategies for improving plant productivity and resilience.
Looking Ahead:
What are the main challenges that we still need to overcome? What are the opportunities provided by accumulating knowledge and advancing technologies?
We need to develop tools that enable spatiotemporal manipulation of specific signaling events, and we are developing such tools using nanobodies, molecular sensors, and chemicals/drugs. We would like to expand our research into non-model plants of economic or ecological importance. To do this, we need funding and people to replicate in crops (e.g. maize) some of the productive proteomic experiments (e.g. proximity labeling and O-glycosylation profiling) that we have done in Arabidopsis. We also need to develop better transformation methods to easily transform plants that are difficult or impossible to transform with current methods, and we are testing some novel ideas.
The rapid development in technologies presents exciting opportunities for life science. For example, structures of nearly all proteins can now be predicted by AlphaFold and visualized by cryoEM. This makes it possible to carry out structure-based drug discovery for plant biology. We are using combinations of virtual and experimental screening approaches to identify chemical inhibitors and modulators of plant proteins, developing chemical tools useful for basic research and agricultural application.
Contact Zhiyong Wang
The Wang Lab strives to push the frontier and hope to one day make a real positive impact on our world. If you are interested in joining us, or supporting us, reach out via email to zwang@carnegiescience.edu.
Protein O-glycosylation is a nutrient-signaling mechanism that plays essential roles in maintaining cellular homeostasis across different species. In plants, SPINDLY (SPY) and SECRET AGENT (SEC) catalyze posttranslational modifications of hundreds of intracellular proteins by O-fucose and O-linked N-acetylglucosamine, respectively. SPY and SEC play overlapping roles in cellular regulation and loss of both SPY and SEC causes embryo lethality in Arabidopsis. Using structure-based virtual screening of chemical libraries followed by in vitro and in planta assays, we identified a SPY O-fucosyltransferase inhibitor (SOFTI). Computational analyses predicted that SOFTI binds to the GDP-fucose-binding pocket of SPY and competitively inhibits GDP-fucose binding. In vitro assays confirmed that SOFTI interacts with SPY and inhibits its O-fucosyltransferase activity. Docking analysis identified additional SOFTI analogs that showed stronger inhibitory activities. SOFTI treatment of Arabidopsis seedlings decreased protein O-fucosylation and caused phenotypes similar to the spy mutants, including early seed germination, increased root hair density, and defect in sugar-dependent growth. By contrast, SOFTI had no visible effect on the spy mutant. Similarly, SOFTI inhibited sugar-dependent growth of tomato seedlings. These results demonstrate that SOFTI is a specific SPY O-fucosyltransferase inhibitor and a useful chemical tool for functional studies of O-fucosylation and potentially for agricultural management.
By directly altering microscopic interactions, pressure provides a powerful tuning knob for the exploration of condensed phases and geophysical phenomena (1). The megabar regime represents an exciting frontier, where recent discoveries include novel high-temperature superconductors, as well as structural and valence phase transitions (2–7). However, at such high pressures, many conventional measurement techniques fail. Here, we demonstrate the ability to perform local magnetometry inside of a diamond anvil cell with sub micron spatial resolution at megabar pressures. Our approach utilizes a shallow layer of Nitrogen-Vacancy (NV) color centers implanted directly within the anvil (8–10); crucially, we choose a crystal cut compatible with the intrinsic symmetries of the NV center to enable functionality at megabar pressures. We apply our technique to characterize a recently discovered hydride superconductor, CeH9 (11). By performing simultaneous magnetometry and electrical transport measurements, we observe the dual signatures of superconductivity: local diamagnetism characteristic of the Meissner effect and a sharp drop of the resistance to near zero. By locally mapping the Meissner effect and flux trapping, we directly image the geometry of superconducting regions, revealing significant inhomogeneities at the micron scale. Our work brings quantum sensing to the megabar frontier and enables the closed loop optimization of superhydride materials synthesis.
BackgroundGenetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. Genetic variation in brassinosteroid-responsive cis-elements likely contributes to trait variation. Pinpointing such regulatory variations and quantitative genomic analysis of the variation in TF-target binding, however, remains challenging. How variation in transcriptional targets of signaling pathways such as the brassinosteroid pathway contributes to phenotypic variation is an important question to be investigated with innovative approaches.ResultsHere, we use a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize. HASCh-seq in the B73xMo17 F1s identifies thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) has been observed for 18.3% of target genes and is enriched in promoter and enhancer regions. About a quarter of the ASB sites correlate with sequence variation in BZR1-binding motifs and another quarter correlate with haplotype-specific DNA methylation, suggesting that both genetic and epigenetic variations contribute to the high level of variation in ZmBZR1 occupancy. Comparison with GWAS data shows linkage of hundreds of ASB loci to important yield and disease-related traits.ConclusionOur study provides a robust method for analyzing genome-wide variations of TF occupancy and identifies genetic and epigenetic variations of the brassinosteroid response transcription network in maize.
Plants often adapt to adverse or stress conditions via differential growth. The trans-Golgi Network (TGN) has been implicated in stress responses, but it is not clear in what capacity it mediates adaptive growth decisions. In this study, we assess the role of the TGN in stress responses by exploring the interactome of the Transport Protein Particle II (TRAPPII) complex, required for TGN structure and function. Together with yeast-two-hybrid screens, this identified shaggy-like kinases (GSK3/AtSKs) as TRAPPII interactors. Kinase assays and pharmacological inhibition provided in vitro and in vivo evidence that AtSKs target the TRAPPII-specific subunit AtTRS120. We identified three GSK3/AtSK phosphorylation sites in AtTRS120. These sites were mutated, and the resulting AtTRS120 phosphovariants subjected to a variety of single and multiple stress conditions. The non-phosphorylatable TRS120 mutant exhibited enhanced adaptation to multiple stress conditions and to osmotic stress whereas the phosphomimetic version was less resilient. This suggests that the TRAPPII phosphostatus mediates adaptive responses to abiotic stress factors. AtSKs are multitaskers that integrate a broad range of signals. Similarly, the TRAPPII interactome is vast and considerably enriched in signaling components. An AtSK-TRAPPII interaction would integrate all levels of cellular organization and instruct the TGN, a central and highly discriminate cellular hub, as to how to mobilize and allocate resources to optimize growth and survival under limiting or adverse conditions.
The urban heat island (UHI) effect is an important topic for many cities across the globe. Previous studies, however, have mostly focused on UHI changes along either the spatial or temporal dimension. A simultaneous evaluation of the spatial and temporal variations is essential for understanding the long-term impacts of land cover on the UHI. This study presents the first evaluation and application of a newly developed spatiotemporal weighted regression framework (STWR), the performance of which was tested against conventional models including the ordinary least squares (OLS) and the geographically weighted regression (GWR) models. We conducted a series of simulation tests followed by an empirical study over central Phoenix, AZ. The results show that the STWR model achieves better parameter estimation and response prediction results with significantly smaller errors than the OLS and GWR models. This finding holds true when the regression coefficients are constant, spatially heterogeneous, and spatiotemporally heterogeneous. The empirical study reveals that the STWR model provides better model fit than the OLS and GWR models. The LST has a negative relationship with GNDVI and LNDVI and a positive relationship with GNDBI for the three years studied. Over the last 20 years, the cooling effect from green vegetation has weakened and the warming effect from built-up features has intensified. We suggest the wide adoption of the STWR model for spatiotemporal studies, as it uses past observations to reduce uncertainty and improve estimation and prediction results.
The recent discovery of SPINDLY (SPY)-catalyzed protein O-fucosylation revealed a novel mechanism for regulating nucleocytoplasmic protein functions in plants. Genetic evidence indicates the important roles of SPY in diverse developmental and physiological processes. However, the upstream signal controlling SPY activity and the downstream substrate proteins O-fucosylated by SPY remain largely unknown. Here, we demonstrated that SPY mediates sugar-dependent growth in Arabidopsis (Arabidopsis thaliana). We further identified hundreds of O-fucosylated proteins using lectin affinity chromatography followed by mass spectrometry. All the O-fucosylation events quantified in our proteomic analyses were undetectable or dramatically decreased in the spy mutants, and thus likely catalyzed by SPY. The O-fucosylome includes mostly nuclear and cytosolic proteins. Many O-fucosylated proteins function in essential cellular processes, phytohormone signaling, and developmental programs, consistent with the genetic functions of SPY. The O-fucosylome also includes many proteins modified by O-linked N-acetylglucosamine (O-GlcNAc) and by phosphorylation downstream of the target of rapamycin (TOR) kinase, revealing the convergence of these nutrient signaling pathways on key regulatory functions such as post-transcriptional/translational regulation and phytohormone responses. Our study identified numerous targets of SPY/O-fucosylation and potential nodes of crosstalk among sugar/nutrient signaling pathways, enabling future dissection of the signaling network that mediates sugar regulation of plant growth and development.
