Hakme Lee

Bio: Hakme Lee is an academic researcher from University of Maryland, College Park. The author has contributed to research in topics: Pulvinus & Proteome. The author has an hindex of 2, co-authored 3 publications receiving 6 citations.

Differentially Expressed Proteins of Soybean (Glycine max) Pulvinus in Light and Dark Conditions

Abstract: Some plant species both track and avoid the sun through turgor changes of the pulvinus tissue at the base of their leaves, maximizing light reception in dim conditions and minimizing cellular damage due to excessive light. Pulvinar response is known to be affected by both diurnally varying environmental factors and circadian patterns. Differential expression of the proteins between light and darkness are not well-known. In this study we used two-dimensional gel electrophoresis and mass spectrometry to separate and identify proteins in the soybean leaf pulvinus that were differentially expressed in the light compared to a dark control. Out of 165 protein spots previously identified (data not shown) 11 were found to have decreased expression in the light and 7 had increased light expression. The proteins that were more highly expressed in the light were mostly stress response proteins, while the under-expressed proteins were categorized as energy proteins. While the higher levels of expression of stress response proteins in the light align with other studies, the under-expressed light proteins require further examination to rule out artefactual results. These findings can provide a better understanding of the circadian pattern of protein expression in the legume pulvinus proteome.

Proteomic analysis of the pulvinus, a heliotropic tissue, in Glycine max

Abstract: Certain plant species respond to light, dark, and other environmental factors by leaf movement. Leguminous plants both track and avoid the sun through turgor changes of the pulvinus tissue at the base of leaves. Mechanisms leading to pulvinar turgor flux, particularly knowledge of the proteins involved, are not well-known. In this study we used two-dimensional gel electrophoresis and liquid chromatography-tandom mass spectrometry to separate and identify the proteins located in the soybean pulvinus. A total of 183 spots were separated and 195 proteins from 165 spots were identified and functionally analyzed using single enrichment analysis for gene ontology terms. The most significant terms were related to proton transport. Comparison with guard cell proteomes revealed similar significant processes but a greater number of pulvinus proteins are required for comparable analysis. To our knowledge, this is a novel report on the analysis of proteins found in soybean pulvinus. These findings provide a better understanding of the proteins required for turgor change in the pulvinus.

Differentially Expressed Proteins of Soybean (Glycine max) Pulvinus in Light and Dark Conditions

Abstract: Some plant species both track and avoid the sun through turgor changes of the pulvinus tissue at the base of their leaves, maximizing light reception in dim conditions and minimizing cellular damage due to excessive light. Pulvinar response is known to be affected by both diurnally varying environmental factors and circadian patterns. Differential expression of the proteins between light and darkness are not well-known. In this study we used two-dimensional gel electrophoresis and mass spectrometry to separate and identify proteins in the soybean leaf pulvinus that were differentially expressed in the light compared to a dark control. Out of 165 protein spots previously identified (data not shown) 11 were found to have decreased expression in the light and 7 had increased light expression. The proteins that were more highly expressed in the light were mostly stress response proteins, while the under-expressed proteins were categorized as energy proteins. While the higher levels of expression of stress response proteins in the light align with other studies, the under-expressed light proteins require further examination to rule out artefactual results. These findings can provide a better understanding of the circadian pattern of protein expression in the legume pulvinus proteome.

Transgenic soybeans and soybean protein analysis: an overview.

Abstract: To meet the increasing global demand for soybeans for food and feed consumption, new high-yield varieties with improved quality traits are needed. To ensure the safety of the crop, it is important to determine the variation in seed proteins along with unintended changes that may occur in the crop as a result various stress stimuli, breeding, and genetic modification. Understanding the variation of seed proteins in the wild and cultivated soybean cultivars is useful for determining unintended protein expression in new varieties of soybeans. Proteomic technology is useful to analyze protein variation due to various stimuli. This short review discusses transgenic soybeans, different soybean proteins, and the approaches used for protein analysis. The characterization of soybean protein will be useful for researchers, nutrition professionals, and regulatory agencies dealing with soy-derived food products.

The functions of foliar nyctinasty: a review and hypothesis.

Abstract: Foliar nyctinasty is a plant behaviour characterised by a pronounced daily oscillation in leaf orientation. During the day, the blades of nyctinastic plant leaves (or leaflets) assume a more or less horizontal position that optimises their ability to capture sunlight for photosynthesis. At night, the positions that the leaf blades assume, regardless of whether they arise by rising, falling or twisting, are essentially vertical. Among the ideas put forth to explain the raison d'etre of foliar nyctinasty are that it: (i) improves the temperature relations of plants; (ii) helps remove surface water from foliage; (iii) prevents the disruption of photoperiodism by moonlight; and (iv) directly discourages insect herbivory. After discussing these previous hypotheses, a novel tritrophic hypothesis is introduced that proposes that foliar nyctinasty constitutes an indirect plant defence against nocturnal herbivores. It is suggested that the reduction in physical clutter that follows from nocturnal leaf closure may increase the foraging success of many types of animals that prey upon or parasitise herbivores. Predators and parasitoids generally use some combination of visual, auditory or olfactory cues to detect prey. In terrestrial environments, it is hypothesised that the vertical orientation of the blades of nyctinastic plants at night would be especially beneficial to flying nocturnal predators (e.g. bats and owls) and parasitoids whose modus operandi is death from above. The movements of prey beneath a plant with vertically oriented foliage would be visually more obvious to gleaning or swooping predators under nocturnal or crepuscular conditions. Such predators could also detect sounds made by prey better without baffling layers of foliage overhead to damp and disperse the signal. Moreover, any volatiles released by the prey would diffuse more directly to the awaiting olfactory apparatus of the predators or parasitoids. In addition to facilitating the demise of herbivores by carnivores and parasitoids, foliar nyctinasty, much like the enhanced illumination of the full moon, may mitigate feeding by nocturnal herbivores by altering their foraging behaviour. Foliar nyctinasty could also provide a competitive advantage by encouraging herbivores, seeking more cover, to forage on or around non-nyctinastic species. As an added advantage, foliar nyctinasty, by decreasing the temperature between plants through its effects on re-radiation, may slow certain types of ectothermic herbivores making them more vulnerable to predation. Foliar nyctinasty also may not solely be a behavioural adaptation against folivores; by discouraging foraging by granivores, the inclusive fitness of nyctinastic plants may be increased.

Analysis of Soybean Seed Proteins Using Proteomics

Abstract: In order to determine the variation of seed proteins that may occur in the crop as a result of genetic modification, accurate and replicable methodology for protein extraction, isolation, and characterization is essential. Modern proteomic tools are being used to study the expression of proteins to examine alterations in protein profiles caused by genetic mutations and environmental stress [2-10]. Proteome analysis is performed using a variety of methods including structural proteomics such as high throughput (HT) X-ray crystallography and HT nuclear magnetic resonance (NMR) spectroscopy; expressional or analytical proteomics such as gel based electrophoresis (IDE, 2DE, 2DIGE), gel-free (LC-MS/MS or multidimensional protein identification technology (Mud PIT), protein chips, DNA chips, mass spectrometry (MS), micro sequencing; and functional or interaction proteomics such as HT functional assays, ligand chips, yeast 2-hybrid, deletion analysis, and motif analysis [11-14]. In this mini review, we discuss some of the expression analysis methodology that we’ve applied to study soybean seed proteins. Because the extraction of soybean seed proteins for accurate 2-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is challenging, we initially optimized protein extraction techniques by comparing different methods. Extraction of protein suitable for 2D-PAGE is sample-dependent and is achieved by optimizing the concentration of chaotropic agents, detergents, reducing agents, buffers, enzymes and ampholytes. Also helpful in this regard are advances in immobile pH gradient (IPG) technology and the development of electrophoretic instruments have improved the reproducibility of protein separation. The availability of commercial IPG strips in linear and nonlinear gradients with multiple narrow pH ranges [15], allows effective protein separation for various downstream analyses. We compared four different solubilization methods (urea/thiourea, urea, modified trichloroacetic acid (TCA)/ acetone and phenol) for extraction of proteins from soybean seeds for subsequent analysis by 2D-PAGE [16]. Our study demonstrated that the modified TCA/acetone method with urea/thiourea solubilization resolved more protein spots than the urea or phenol extractions. Using the phenol/urea method, resolution of proteins was generally poor and spots diffuse in the high molecular weight region of the gel, particularly when separating the proteins at pH 4.0 to 7.0. Moreover, while overall protein separation was similar in the TCA/acetone and urea/thiourea methods, low molecular weight proteins were more consistently resolved with the TCA/acetone method. In addition, characterization of low abundant proteins is a challenge because they are often masked by highly abundant proteins. Recently, Boschetti and Righetti [17] published a review of plant proteomic methods to isolate

Differential proteomics of Picrorhiza kurrooa Royle ex Benth. in response to dark stress.

Abstract: Picrorhiza (Picrorhiza kurrooa Royle ex Benth.) an important medicinal herb of western Himalayan region has been used to treat various diseases and disorders. Over-harvesting and lack of cultivation has led to its entry in Red Data Book as an endangered species. Further, its very restrictive habitat and lesser biomass production are major limitations for bringing it under commercial cultivation. All these issues necessitate deeper insights into mechanisms governing its growth and interaction with the environmental cues. Light may be one of the important factors to be studied for its role in regulating growth and adaptation of Picrorhiza as in natural habitat it prefers shady niches. Keeping this in view, proteome of Picrorhiza kept under light vis-a-vis under dark was analysed and compared. Leaf as well as root proteome of Picrorhiza was studied. Denaturing two dimensional gel electrophoresis and mass spectrometry techniques were used to detect and identify differentially expressed proteins, respectively. Twenty two proteins from leaf and 25 proteins from root showed differential expression levels under dark and light conditions. Among the differentially expressed proteins, majority were those involved in metabolism, protein synthesis, and stress and defense response. Other differentially expressed proteins were those involved in photosynthetic process, photorespiration and few proteins were with unknown function indicating that many different processes work together to establish a new cellular homeostasis in response to dark and light conditions. Proteins found to be differentially expressed under light vis-a-vis dark conditions suggested a range of biochemical pathways and processes being associated with response of plant to dark conditions. The identified proteins may be utilized for developing strategies for improving the biomass production/performance of Picrorhiza under varied light/dark habitats.

Daily heliotropic movements assist gas exchange and productive responses in DREB1A soybean plants under drought stress in the greenhouse.

Abstract: Drought stress is one of the most severe environmental constraints on plant production. Under environmental pressures, complex daily heliotropic adjustments of leaflet angles in soybean can help to reduce transpiration losses by diminishing light interception (paraheliotropism), increase diurnal carbon gain in sparse canopies and reduce carbon gain in dense canopies by solar tracking (diaheliotropism). The plant materials studied were cultivar BR 16 and its genetically engineered isoline P58, ectopically overexpressing AtDREB1A, which is involved in abiotic stress responses. We aimed to follow the movements of central and lateral leaflets in vegetative stages V7-V10 and reproductive stages R4-R5, integrating the reversible morphogenetic changes into an estimate of daily plant photosynthesis using three-dimensional modeling, and to analyze the production parameters of BR 16 and P58. The patterns of daily movements of central leaflets of BR 16 in V7-V10 and R4-R5 were similar, expressing fewer diaheliotropic movements under drought stress than under non-limiting water conditions. Daily heliotropic patterns of lateral leaflets in V7-V10 and R4-R5 showed more diaheliotropic movements in drought-stressed P58 plants than in those grown under non-limiting water conditions. Leaf area in R4-R5 was generally higher in P58 than in BR 16. Drought significantly affected gas exchange and vegetative and reproductive architectural features. DREB1A could be involved in various responses to drought stress. Compared with the parental BR 16, P58 copes with drought through better compensation between diaheliotropic and paraheliotropic movements, finer tuning of water-use efficiency, a lower transpiration rate, higher leaf area and higher pod abortion to accomplish the maximum possible grain production under continued drought conditions.