中研院植微所「暑期大學生培育計畫」

報名期間：即日起~4/30

線上報名：https://internship.ipmb.sinica.edu.tw/program

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International Master Program in Plant and Microbial Biology, National Chung Hsing University (NCHU)

Welcome to all enthusiasts of plants and microorganisms. Multidiscipline Faculty Members: Institute of Plant and Microbial Biology, Academia Sinica-- College of Agriculture and Natural Resources, NCHU-- College of Life Sciences, NCHU

Enrollment for Fall 2025, Semester starts at Sep 2025

Application Duration: 2024/12/15~2025/3/20

Document Review (in English)

Admission Announcement: 2025/5/31

Application Procedure

https://reurl.cc/L5p083

IMPPMB Website

https://imppmb.email.nchu.edu.tw/

Imagine you are a skilled spy trying to sneak through customs. Keeping a low profile to avoid unnecessary attention is key.

The plant immune system has developed a sophisticated strategy to detect foreign microbes by recognising specific molecules produced by the bacteria. A recent study from Ka-Wai Ma's laboratory at IPMB has uncovered a group of commensal bacteria called Xanthomonadales that have the ability to hide from plant recognition. Dr. Ma explains their study as follows. "Think of these commensal bacteria as skilled spies - rather than raising alarm or suspicion, they are very good at hiding. From a more scientific point of view, these bacteria can use tools, probably hydrolytic enzymes (analogous to a pair of scissors), to cut out conspicuous features to tell plants that this is a bacterium. More importantly, these scissors help not only the producer but also other microbes to hide. Like wearing a Harry Potter invisibility cloak. These bacteria can also use a second mechanism to suppress the plant's immune system, but in a more brutal way, by directly suppressing the immune system, just like knocking out the customs officer. 

Why is this important? Just like in the gut, good and bad bacteria coexist. The plant's immune system acts as the first line of defence against pathogens. Although commensals are not pathogens, they also develop the ability to suppress plant immunity, indirectly affecting plant resistance to pathogens. So these commensal bacteria are not as harmless as we thought. Understanding this interaction could lead to better ways of controlling pathogens and understanding the importance of these commensal bacteria in modulating plant immunity. So next time you see a healthy plant, remember: a microscopic community is working hard to keep it that way!

Ordon et al (2025) Conserved immunomodulation and variation in host association by Xanthomonadales commensals in Arabidopsis root microbiota. Nature Plants.

Topic: Plant cytokinesis – An alternative strategy to divide the cell

Speaker: Dr. Gerd Jürgens

Date: 15:00, March 12th (Wednesday), 2025

Venue: Auditorium A134 & A133 (Synchronous Broadcasting), Agricultural Technology Building, Institute of Plant and Microbial Biology, Academia Sinica

Cyanobacteria are diverse phototrophic microbes with ecological importance and potential for biotechnology applications. Among them, thermophilic species from hot springs have garnered particular attention for their ability to produce thermostable enzymes and proteins with promising industrial uses.

To advance research on thermophilic cyanobacteria, Drs. Chih-Horng Kuo and Hsiu-An Chu from the Institute of Plant and Microbial Biology, Academia Sinica, have established a long-term collaboration. In their latest project, the team conducted extensive sampling of hot springs across Taiwan to isolate novel strains and perform comprehensive genomic analyses.

Their study revealed novel insights into the genomic divergence at species and subspecies levels within these thermophilic cyanobacteria. Additionally, the team identified a large number of population-specific genes that have undergone selective sweeps, shedding light on the adaptive mechanisms of these organisms. Together, these findings provide a population genomics perspective on a hot spring cyanobacterial species in Taiwan.

Taken together, this work provided a population genomics perspective on a hot spring cyanobacterial species in Taiwan. Beyond advancing our understanding of microbial genomics and evolution, the strains collected and genome sequences generated in this project provide valuable materials for future development and utilization of biological resources.

Beyond enriching our understanding of microbial genomics and evolution, the strains collected and genome sequences generated through this project represent valuable resources for future biotechnological development and applications.

This research was published in Botanical Studies, an international journal affiliated with the Institute of Plant and Microbial Biology, Academia Sinica. The co-authors include Hsin-Ying Chang and Hsi-Ching Yen, both are research assistants mentored by Dr. Chih-Horng Kuo. The project was funded by Academia Sinica.

Chang HY, Yen HC, Chu HA, Kuo CH (2024) Population genomics of a thermophilic cyanobacterium revealed divergence at subspecies level and possible adaptation genes. Botanical Studies 65:35.

The core of taxonomy lies in grouping and naming organisms, establishing a foundation for biological research and scientific communication. With advancements in genomics, genome sequence analysis has become an essential tool for classifying prokaryotes at the level of species. However, how to apply genome-based analyses to higher taxonomic levels remains a subject of debate in the scientific community.

To address this issue, an international collaborative team led by Dr. Chih-Horng Kuo of the Institute of Plant and Microbial Biology, Academia Sinica, conducted a systematic genomic analysis using species from the class Mollicutes as study materials. The team integrated gene content differentiation analysis, data visualization, and phylogenetic relationships to comprehensively explore how natural taxonomic groups form and correspond to the genus level.

This study revealed that recent taxonomic revisions within the class Mollicutes have tended toward over-splitting. Several of the newly described or emended genera lack clear differentiations in gene content and ecology. Also, some species were misclassified into inappropriate genera. These findings provide a solid basis for future taxonomic revisions, ensuring a more reasonable and precise classification and nomenclature of these important pathogens. Moreover, the bioinformatic concepts and methods developed in this study can be broadly applied to the classification of other prokaryotes or different taxonomic levels.

This work was published in Microbial Genomics, a journal of the Microbiology Society. The authors include Xiao-Hua Yan, Shen-Chian Pei, and Hsi-Ching Yen from Chih-Horng Kuo’s laboratory, along with collaborators from France, Canada, and the United States. Among the team members, Alain Blanchard, Gail E. Gasparich, and Chih-Horng Kuo are members of the Subcommittee on the Taxonomy of Mollicutes under the International Committee on Systematics of Prokaryotes (ICSP). This research project was primarily funded by Academia Sinica.

Yan XH, Pei SC, Yen HC, Blanchard A, Sirand-Pugnet P, Baby V, Gasparich GE, Kuo CH* (2024) Delineating bacterial genera based on gene content analysis: a case study of the Mycoplasmatales–Entomoplasmatales clade within the class Mollicutes. Microbial Genomics 10:001321.

Although it is well perceived that conserved ubiquitin receptors play a vital role in recognition and targeting ubiquitinated cellular regulators to proteasome for degradation, solid evidence to support the in vivo importance of ubiquitin-binding activities for these ubiquitin receptors in vivo is scarce. Dr. Hongyong Fu’s group reported previously the ubiquitin binding activities of the major ubiquitin receptor RPN10 is dispensable for in vivo functions observed with rpn10-2 null mutant. A new report just published in Int J Mol Sci from Dr. Fu’s group confirms this idea again by observing that a C-terminal truncated RPN10 harboring only a vWA domain and missing all ubiquitin binding motifs is fully functional in vivo. Instead, all evidence provided in this report support RPN10 plays an important structural role in the 26S proteasome in vivo. First, a site-specific variant, RPN10-11A, that likely has a destabilized vWA domain could only partially rescue the rpn10-2 growth defects and is not integrated into 26S proteasomes. Second, native polyacrylamide gel electrophoresis of the 26S proteasomes isolated from various rpn10-complemented lines showed the correlation of the extent of reduced abundance of the double-capped 20S proteasomes with the severity of growth defects. In addition, mass spectrometry analyses of the 26S proteasomes isolated from rpn10 showed increased integration of specific subunit paralogues and increased association of ECM29, a well-known factor critical for quality checkpoints by binding and inhibiting aberrant proteasomes. In the same report, extensive Y2H and GST-pulldown analyses identified RPN2-binding residues on RPN13 that overlapped with ubiquitin-binding and a UCH2-binding region in the RPN13 C-terminus (246–254). Interestingly, an analysis of homozygous rpn10-2 segregation in a rpn13-1 background harboring RPN13 variants defective for ubiquitin binding and/or RPN2 binding supports the criticality of the RPN13–RPN2 association in vivo.

Lin, S.-Y., Lin, Y.-L., Usharani, R., Radjacommare, R., and Fu, H. The structural role of RPN10 in the 26S proteasome and an RPN2-binding residue on RPN13 are functionally important in Arabidopsis. Int. J. Mol. Sci. 2024, 25, 11650.