Institute of Plant and Microbial Biology

│PI Information│Research Interests│Publications│Lab Members│

ON GOING PROJECT

Biological functions of soybean seed maturation proteins
Studies on rice functional genomics
Analysis of wild soybean species collected in Taiwan

Biological functions of soybean seed maturation proteins

Late embryogenesis abundant (LEA) proteins are synthesized in seeds at a late stage of development. During this stage, the newly synthesized seed protein profile is very different from that of the mid-development stage and is associated with desiccation tolerance. LEA proteins have been widely reported from organisms including prokaryotes, fungus, plant and animal kingdoms and are classified into 6 groups. We use soybean seed maturation proteins as a model system to study the physiological function and biochemical properties of LEA proteins, with emphasis on group III and IV. For instances, GmPM16 proteins, a type IV protein, undergo dehydration-induced conformational changes and adopt high amount α -helical structures. It interacts with sugar and form tightly glassy matrixes in the dry state. The protein-sugar glasses may play a role in reducing cellular damage in drying seeds by changing protein conformation as well as forming tight cellular glassy matrices.

Another two members of soybean group 4 LEA proteins; the basic GmPM1 and the acidic GmPM28, were also studied by circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy. The spectra and protein folding parameters of both proteins revealed large amounts of disordered secondary structures in the fully hydrated state. Therefore, we suggest that the soybean group 4 LEA proteins in an aqueous phase are “natively unfolded proteins.” Conformational changes of GmPM1 or GmPM28 could be observed under hydrophobic or dry conditions. After fast or slow drying, the two proteins had slightly higher proportions of defined secondary structures (α-helix and β-sheet), from 30% to 49% for GmPM1, and from 34% to 42% for GmPm28. Nevertheless, after this conformational change, the interaction between non-reducing sugars and both soybean group 4 LEA proteins still occurred. The two proteins possessed the ability to affect the conformations of poly-l-lysine after slow drying, but this ability was lost after they aggregated upon storage at room temperature. Our work suggests that soybean group 4 LEA proteins play a role as a molecular chaperone during dehydration.

Studies on rice functional genomics

As part of the effort for rice functional genomics research, a team was funded to address gene functions in Taiwan using T-DNA knock-out and activation-tagging strategy. Stable insertion lines are generated containing random insertions of T-DNA in japonica rice cv. Tainung 67, which is one of the most popular cultivars in Taiwan. Currently a more than 60,000 insertion line collection is created, with more than 25,000 flanking sequence tags (FST) available. The name for the database is Taiwan Rice Insertional Mutants (TRIM), with the URL address of http://trim.sinica.edu.tw/.

The T0 and T1 plants of the TRIM population were grown in net “houses” for two cropping seasons each year since 2003, with the mutant phenotypes recorded. Detailed data describing growth and development of these plants, in 11 categories and 65 subcategories, over the entire 4-month growing season are available in a searchable database, along with the genetic segregation information and flanking sequence data. With the detailed data from more than 20,000 T1 lines and 12 plants per line, we estimated the mutation rates of the T1 population, as well the frequency of the dominant T0 mutants. The correlations among different mutation phenotypes are also calculated. Together, the information about mutant lines, their integration sites, and the phenotypes make this collection, the Taiwan Rice Insertion Mutants (TRIM), a good resource for rice phenomics study.

We also estimated the SNP rate between Tainung 67 and Nipponbare, constructed two BAC libraries of Tainung67, and analyzed the transcriptome of developing rice anthers and maturing rice seeds.

Analysis of wild soybean species collected in Taiwan

The genus Glycine Willd, consists of many species in two subgenera, Soja and Glycine. The subgenus Soja includes the diploid cultivated soybean, G. max and its wild relative, G. soja. The subgenus Glycine includes 20 species, and all species within the subgenus are perennial. It is shown that Taiwan is the southernmost of the distribution for the annual wild soybean. For the perennial species, two of them have been suggested to be the probable ancestor of G. soja – G. tomentella and G. tabacina. Taiwan is the northernmost of the distribution for these two perennial species and the southernmost of that of G. soja. The collection and study of wild soybean and their relatives in Taiwan and the adjacent islands are thus very important to develop and understand of their evolution and relationships. In addition, many of these species are also tolerant to disease, insects and several kinds of environmental stresses such as water stress or salt stress.

We used seed morphology, 2D gel protein profiles, cytogenetics, LEA gene sequences to reveal the relationship among cultivated and wild soybean species.

│PI Information│Research Interests│Publications│Lab Members│

Selected Publications

Full publication list

Chern CG, .. (another 21 authors).., Hsing YI. (2007). A rice phenomics study - phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population. Plant Mol Biol. 65: 427-438.
Hour AL, YC Lin, PF Li, TY Chow, WF Lu, FJ Wei, and YIC Hsing. 2007. Detection of SNPs between Tainung 67 and Nipponbare rice cultivars. Bot. Studies (in press)
Hsing, YI, Chern, CG, Fan, MJ ..(Another 26 authors)..and Yu S-M (2007) A Rice gene activation/knockout library for high throughput functional genomics analysis. Plant Mol Biol. l63: 351-364.
International Rice Genome Sequencing Project. (2005). The map-based sequence of the rice genome. Nature 436: 793-800. Author lists: Academia Sinica Plant Genome Center ( ASPGC) TY Chow, HH Chen, MC Chung, CS Chen, JF Shaw, HP Wu, KJ Hsiao, YT Chao, MK Chu, CH Cheng, AL Hour, PF Lee, SJ Lin, YC Lin, JY Liou, SM Liu, YI Hsing.
Lin, YR, Chow TY, Luo M, Kudrna D, Lin CC, Wing RA, Hsing YI. (2006). Two Highly Representative Rice BAC Libraries of Japonica cv Tainung 67, Suitable for Rice Structural and Functional Genomic Research. Plant Sci. 170: 889-896.
Lu CA, Lin CC, Lee KW, Chen JL, Huang LF, Ho SL, Liu HJ, Hsing YI, Yu SM. 2007. The SnRK1A Protein Kinase Plays a Key Role in Sugar Signaling during Germination and Seedling Growth of Rice. Plant Cell 19: 2484-99.
Rice Annotation Project, Itoh T, ..(Another 93 authors).. Sasaki T. 2007. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17:175-83.
Shih, M.D.,S.C. Lin, J. S. Hsieh, C.H. Tsou, T.Y. Chow, T.P Lin and Y.I.C. Hsing. (2004). Gene cloning and characterization of a soybean (Glycine max L.) LEA protein, GmPM16. Plant Mol. Biol. 56:689-703
Ueguchi-Tanaka, M., Ashikari, M., Nakajima M., Itoh H., Katoh E., Kobayashi M., Chow T., Hsing Y., Kitano H., Yamaguchi I., Matsuoka M. (2005). Gibberellin insensitive dwarf 1 encodes soluble receptor for gibberellin. Nature 437:693-698.
Yu SM, Ko SS, Hong CY, Sun HJ, Hsing YI, Tong CG, Ho TH. (2007). Global functional analyses of rice promoters by genomics approaches. Plant Mol Biol. 65: 417-425.