Jae-Woong Yu

Genome-wide analysis and expression profiling of the Solanum tuberosum aquaporins.

Aquaporins belongs to the major intrinsic proteins involved in the transcellular membrane transport of water and other small solutes. A comprehensive genome-wide search for the homologues of Solanum tuberosum major intrinsic protein (MIP) revealed 41 full-length potato aquaporin genes. All potato aquaporins are grouped into five subfamilies; plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), NOD26-like intrinsic proteins (NIPs), small basic intrinsic proteins (SIPs) and x-intrinsic proteins (XIPs). Functional predictions based on the aromatic/arginine (ar/R) selectivity filters and Frogers positions showed a remarkable difference in substrate transport specificity among subfamilies. The expression pattern of potato aquaporins, examined by qPCR analysis, showed distinct expression profiles in various organs and tuber developmental stages. Furthermore, qPCR analysis of potato plantlets, subjected to various abiotic stresses revealed the marked effect of stresses on expression levels of aquaporins. Taken together, the expression profiles of aquaporins imply that aquaporins play important roles in plant growth and development, in addition to maintaining water homeostasis in response to environmental stresses.

Evaluation of abiotic stress tolerance in transgenic potato plants with reduced expression of PSII manganese stabilizing protein.

Manganese stabilizing protein (MSP) is an important component of the Photosystem II (PSII) oxygen evolving complex. In our previous work, transgenic potato plants with reduced expression of MSP (MSP-As) were developed and their physiological and biochemical responses were studied. In this report, we address the response of MSP-As plants toward salinity, heavy metal and osmotic stresses. MSP-As plants treated with NaCl, ZnCl(2) or mannitol solution showed significant level of tolerance under all the stress conditions. Specific enzyme activities of major ROS-scavenging enzymes were found significantly higher in MSP-As plants than the control plants. MSP-As plants accumulated increased levels of proline and low molecular weight metabolites such as ascorbate and α-tocopherol, which indicated that these plants were much more resistant to stress compared to the corresponding control plants. The primary photochemical efficiencies and the OJIP kinetics analyses further confirmed that MSP-As plants were in better optimal health under stress compared to the control plants. Although the exact reason behind the increased stress tolerance in stressed MSP-As plants is unclear, our results strongly indicate the role of MSP of unknown function in abiotic stress tolerance.

Reverse transcriptase domain sequences from Mungbean (Vigna radiata) LTR retrotransposons: Sequence characterization and phylogenetic analysis

The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were amplified from mungbean (Vigna radiata) genome using degenerate primers, cloned and sequenced. Among these 34% and 65% of respective clones of copia and gypsy RT sequences possessed stop codons or frame-shifts or both. The RT sequences corresponding to both the groups exhibit significant levels of heterogeneity. Presence of mungbean copia and gypsy RT sequences in other papilionoid legumes of the same (Phaseoleae) and different lineages (Loteae, Trifoleae, Cicereae) indicates existence of these elements prior to the radiation of papilionoid legumes and also supports the recent interpretations of close relationship between Phaseoleae and Loteae tribes of Papilionoideae subfamily. On the other hand significant homologies of some mungbean copia as well as gypsy RT sequences with those of unrelated plant species suggest their origin from different plant lineages and also that heterogeneous population of related elements were already existed throughout (even before the divergence of monocot and dicot) the evolution of these genera from their common ancestor.

Chlorophyll a fluorescence transient analysis of transgenic potato overexpressing D-galacturonic acid reductase gene for salinity stress tolerance

L-Ascorbate plays a vital role in the alleviation of salinity stress in crop plants. Overexpression of the ascorbate pathway enzyme D-galacturonic acid reductase in transgenic potato plants confers improved tolerance to various abiotic stresses. These transgenic potato plants were further studied for their primary photosynthetic performances under salinity stress. The changes in primary photochemistry of PSII induced by salinity stress were studied using JIP-test. Analysis of the fast phase chlorophyll a fluorescence transients indicated that there was a differential effect of salinity stress on different sites of the photosynthetic machinery. The transgenic potato leaves exhibited a gain in the ability for restraining the energy loss when they were imposed by salinity stress. These observations suggest that under salinity stress, the photosynthetic energy conservation in the transgenic plants was more effective than in the wild-type plants.

A study on relative abundance, composition and length variation of microsatellites in 18 underutilized crop species

In the present work, genomic DNA libraries for 18 underutilized crop species (including 11 dicot and 7 monocot species) were enriched for several di- and tri- nucleotide microsatellites by using an optimized procedure. About 500–960 clones from each library were sequenced and all the sequences were characterized to have a comparative look on relative abundance, composition and length variations of perfect microsatellites among different crops. Sequence analysis revealed contrasting differences in the abundance of di- and tri-nucleotide microsatellites with the predominance of tri-nucleotide microsatellites in 11 crops and that of di-nucleotides in other 8 crops. Among di-nucleotide microsatellites, AG/GA class was the most abundant in all the crops except for four crops in which AC/CA class was predominant. Among tri-nucleotide repeats, AGC/GCA/CAG class was the most abundant in eight crops followed by AGG/GGA/GAG class in four crops, whereas in the remaining six crops, the most abundant class was highly variable. The longest di- and tri-nucleotide repeats were observed in Chinese cabbage and mungbean with the average lengths of 70 and 57 base pairs, respectively. These observations revealed species-specific in the distributions of microsatellite repeat motifs. The present study provides highly valuable information that can be useful in targeted development of specific microsatellites markers for genetic analysis of these underutilized crops.

Dynamic proteomic profile of potato tuber during its in vitro development.

Potato tuberization is a complicated biochemical process, which is dependent on external environmental factors. Tuber development in potato consists of a series of biochemical and morphological processes at the stolon tip. Signal transduction proteins are involved in the source-sink transition during potato tuberization. In the present study, we examined protein profiles under in vitro tuber-inducing conditions using a shotgun proteomic approach involving denaturing gel electrophoresis and liquid chromatography-mass spectrometry. A total of 251 proteins were identified and classified into 9 groups according to distinctive expression patterns during the tuberization stage. Stolon stage-specific proteins were primarily involved in the photosynthetic machinery. Proteins specific to the initial tuber stage included patatin. Proteins specific to the developing tuber stage included 6-fructokinase, phytoalexin-deficient 4-1, metallothionein II-like protein, and malate dehydrogenase. Novel stage-specific proteins identified during in vitro tuberization were ferredoxin-NADP reductase, 34 kDa porin, aquaporin, calmodulin, ripening-regulated protein, and starch synthase. Superoxide dismutase, dehydroascorbate reductase, and catalase I were most abundantly expressed in the stolon; however, the enzyme activities of these proteins were most activated at the initial tuber. The present shotgun proteomic study provides insights into the proteins that show altered expression during in vitro potato tuberization.

Molecular evolution and functional divergence of X-intrinsic protein genes in plants.

X-intrinsic proteins (XIPs) are a novel class of major intrinsic proteins found in diverse organisms. Recently, XIP genes have been reported to be involved in the transport of a wide range of hydrophobic solutes; however, the evolutionary forces driving their structural and functional divergence in plants are poorly understood. In the present study, comprehensive bioinformatics analyses were performed to gain insight into the molecular and evolutionary mechanisms driving this structural and functional diversification. Phylogenetic analyses have revealed the major lineage-specific expansions of XIP genes in plants. Within the eudicots, XIP genes have diverged into Asterid and Rosid-specific phylogenetic lineages and have also undergone several independent duplications during the course of evolution. Investigation of functional divergence at the protein level showed evidence for shifting evolutionary rate and/or altered constraints on the physiochemical properties of specific amino acid sites following gene duplication. Selection pressure analyses suggest that purifying selection is the predominant evolutionary force acting on the XIP gene subfamily, along with episodic positive selection. However, only a few amino acid sites were found to be subjected to such episodic positive selection. Furthermore, protein functional divergence analysis has identified critical amino acid residues, which must be validated by future experimental studies, that could provide new insights into the role of XIPs in transport of a wide range solutes of physiological importance.

Effect of LED mixed light conditions on the glucosinolate pathway in brassica rapa

In the agricultural industries, LEDs are used as supplementary, as well as main lighting sources in closed cultivation systems. In cultivation using artificial light sources, various light qualities have been tried to supplement fluorescent lamps to promote plant growth and metabolism. Microarray analysis of Brassica rapa seedlings under blue and fluorescent mixed with blue light conditions identified changes in three genes of the glucosinolate pathway. This attracted attention as functional materials highly expressed 3.6-4.6 fold under latter condition. We selected four more genes of the glucosinolate pathway from the Brassica database and tested their expression changes under fluorescent light mixed with red, green, and blue, respectively. Some genes increased expression under red and blue mixed conditions. The Bra026058, Bra015379, and Bra021429; the orthologous genes of CYP79F1, ST5a, and FMOGS-OX1 in Arabidopsis, are highly expressed in Brassica rapa under fluorescent mixed with blue light conditions. Further, Bra029355, Bra034180, Bra024634, and Bra022448; the orthologous genes of MAM1, AOP3, UGT74B1, and BCAT4 in Arabidopsis, are highly expressed in Brassica rapa under fluorescent mixed with red light conditions. The various light conditions had unique effects on the varieties of Brassica, resulting in differences in glucosinolate synthesis. However, in some varieties, glucosinolate synthesis increased under mixed blue light conditions. These results will help to construct artificial light facilities, which increase functional crops production.