Shi Mingzhe Distinguished Researcher

E-mail: mcshih@gate.sinica.edu.tw
Phone: (02) 2789-9403

Distinguished Researcher and Chairman of the Preparatory Committee of the Southern District of Academia Sinica, Bachelor of Biology, Donghai University (1976)
PhD in Genetics, University of Iowa (1978-1983)
Postdoctoral research in the Department of Genetics, Harvard University (1984-1988)
Assistant Professor, Department of Biology, University of Iowa (1988-1994)
Associate Professor, Department of Biology, University of Iowa (1994-2003)
Director of the Center for Comparative Genomics, University of Iowa (2005-2007)
Professor, Department of Biology, University of Iowa (2003-2009)
Distinguished researcher and director of the Agricultural and Health Center of Academia Sinica (2008-2016)
Distinguished researcher and secretary-general of the Academia Sinica Agriculture and Health Center (2016-present)

Office: B208, Building B, Agricultural Science Building

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research direction

The molecular mechanism of Arabidopsis and rice hypoxia response The main goal of this project is to explore the molecular mechanism of plant response to hypoxia caused by flooding, with the hope that it can be used to improve the flooding resistance of crops in the future. In the recent research results of the laboratory, we found that the response of plants in the two stages of submergence hypoxia and reoxygenation are the critical periods that determine the tolerance of plants to hypoxia stress (Fig. 1 ), and further pointed out that ethylene is the two critical periods. The main message transmitter that controls gene expression and metabolism. Plants also induce a large number of expressions of the key transcription factor WRKY22 to prevent bacterial infection during flooding or after the flood recedes. On the other hand, we found through proteomics analysis that in the early stage of flooding and hypoxia, the protein-stimulated (SnRK1) phosphate chain reaction regulates hypoxia metabolism and protein translation of key hypoxia response genes.

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Fig. 1 Schematic of our studies in flooding stress.

Based on the above findings, the laboratory is in-depth analysis of the molecular mechanism of SnRK1 regulating protein translation and how ethylene regulates the metabolic flow during hypoxia and reoxygenation under the adversity of Arab mustard flooding (Fig. 2 ). In addition, we also conduct research on upstream molecules that can activate immune and disease-related gene expressions (such as WRKY22) at the initial stage of flooding and hypoxia. We have found that many gene mutations in the lectin receptor-like kinases (LecRKs) family affect the response of plants to disease resistance and flooding tolerance. In the future, we will further analyze whether LecRKs are receptors for the expression of genes that induce immune response under submerged water.

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Fig.2 Model of TCA cycle replenishment in response to reoxygenation

Sub1A1 is a known key flood resistance gene in rice. Its gene expression is regulated by flooding and belongs to the ethylene response factor VII (ERFVII) transcription factor family. The ERFVII family proteins all have N-degron (Met- Cys-Gly-Gly) sequence. In an aerobic environment, the protein with this sequence will be identified and degraded by the N-end rule pathway, which has the ability to sense oxygen concentration; in anoxic environment, the activity of the N-end rule pathway is inhibited, and the ERFVII protein accumulates steadily. However, Sub1A1 is currently the only known ERFVII transcription factor that has N-degron but is not degraded by the N-end rule pathway. On the other hand, we found two ERFVII transcription factors, ERF66 and ERF67, whose proteins were identified by N-end rule and their gene expression was regulated by Sub1A1 under submerged water. It shows that ERF66 and ERF67 proteins not only stably accumulate under submerged water, but also amplify the water-resistant response regulated by ERF66 and ERF67 through the transcriptional regulation of Sub1A. Combining the above findings, we propose a new flood tolerance regulation pathway for Sub1A, ERF66 and ERF67 through gene expression and N-end rule regulation. At present, we are exploring in depth how Sub1A protein is not regulated by N-end rule and the information pathway regulated by Sub1A-ERF66 / ERF67.

Construction of Taiwan Phalaenopsis Functional Gene Database and Research on Biotechnology

The main goal of this project is to establish a complete genome database of Taiwan Phalaenopsis aphrodite. Grandma from Taiwan is the breeding parent of the white Phalaenopsis with a high market share. We plan to use this genomic database combined with molecular biology breeding and gene transfer technology to create a new platform for orchid breeding. At present, our team has established high-quality Taiwanese grandmother genome sequence sketches and linkage maps through next-generation sequencing analysis, and combined BAC contig assembly and marker typing technology to establish high coverage and low error rates Draft of the genome sequence. The draft genome sequence that meets this standard is suitable for routine gene sequence analysis and search (Fig. 3 ).
On the other hand, we are now also constructing transcript and metabolite data for orchid flower pigments, fragrance synthesis and developmental regulation. It is hoped that this information can be used to select Phalaenopsis with a short growth cycle, different flower color and fragrance, and only a short period of low temperature to induce flowering.

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Fig.3 Orchidstra 2.0

Biological pesticide development

Pseudomonas taiwanensis is a new type of soil bacteria of the genus Pseudomonas sieved from the soil in northern Taiwan and can grow on a medium using shrimp shell meal as a single carbon and nitrogen source. Desorption/ionization imaging mass spectrometry) and Tn5 mutation library analysis, we found that P. taiwanensis can release a new type of pyoverdine to inhibit ( Xoo ) growth via the Type 6 Secretion System (Fig. 4). In addition to resistance to rice bacterial blight, we also found antifungal compounds and insect-resistant proteins in P. taiwanensis and other soil microorganisms. In the future, we will develop P. taiwanensis and other microorganisms as sources of biopesticides and cooperate with biotech companies to conduct field trials in order to expand to practical agricultural applications.

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Fig.4 Schematic of the pyoverdine secretion pathways in P. taiwanensis .