Ku and Sebé-Pedrós 2019 Philosophical Transactions of the Royal Society B

Single-cell RNA sequencing enables quantification and characterization of gene transcripts in individual cells — the basic structural and functional unit of life. Recent advances in its methodology and efficiency have revolutionized our understanding of cell types and developmental processes in multicellular organisms, particularly vertebrates. As shown in a few studies, the same approach can also be applied to microbial eukaryotes, or protists, which encompass the vast majority of eukaryotic diversity and are integral components of various ecosystems. In this article, Chuan Ku at IPMB and Arnau Sebé-Pedós at the Centre for Genomic Regulation (CRG) in Barcelona reviewed the current methods of single-cell RNA sequencing and discussed its potential and challenges in studies on microbial eukaryotes. Single-cell RNA sequencing is divided into key steps to provide a quick overview for researchers interested in this technology, with special focus on possible technical difficulties for diverse unicellular eukaryotes. With newly available sequencing platforms and analysis tools, they further offered future perspectives on how transcriptomic information of isolated single cells can facilitate studies on cellular states and microbial interactions in both simple lab cultures and complex field communities. This article is part of the theme issue “Single cell ecology” published on October 7 in Philosophical Transactions of the Royal Society B: https://royalsocietypublishing.org/doi/10.1098/rstb.2019.0098

Cho et al., 2019, Front Microbiol

Phytoplasmas are a group of obligate parasitic bacteria with great impact on agriculture. Due to the difficulties involved in studying uncultivated bacteria, genomics tools have been adopted to investigate their biology. In this work, we conducted whole-genome sequencing of two phytoplasma strains in Taiwan for comparative analysis at the levels of population and species. The results indicated that these two strains collected from different plant hosts (i.e., periwinkle and green onion) have a genome-wide sequence identity of >99.9% and could be considered as the same species. Comparison with a previous population genomics study on phytoplasmas infecting the same host (i.e., maize) but collected over a much longer geographical distance suggested that differentiations in plant hosts may be more important in facilitating genetic divergence. For comparative genomics at the putative species or sub-species levels, the results indicated that these highly reduced genomes are extremely dynamic. In addition to providing further support and more detailed information regarding the impact of mobile genetic elements on the genome evolution of these bacteria, we found that duplication of chromosomal segments and differential gene losses are also important evolutionary processes. Finally, horizontal transfer of effector genes among lineages may be linked to diversification and adaptation.

This work is done in collaboration between Dr. Chih-Horng Kuo and Prof. Chan-Pin Lin (National Taiwan University). The first author Ms. Shu-Ting Cho is a Project Manager in the Kuo lab. The manuscript was published as a part of a special topic “Mollicutes: From Evolution To Pathogenesis” (https://www.frontiersin.org/research-topics/9908/mollicutes-from-evolution-to-pathogenesis) hosted by Frontiers in Microbiology (https://doi.org/10.3389/fmicb.2019.02194).

Cho ST, Lin CP, Kuo CH* (2019) Genomic characterization of the periwinkle leaf yellowing (PLY) phytoplasmas in Taiwan. Frontiers in Microbiology 10: 2194. DOI: 10.3389/fmicb.2019.02194

Lin et al., 2019, Plant Physiology

The red/far-red light photoreceptor phytochrome plays vital roles in plant growth and development. It senses and optimizes the gene expression at different level in response to the changing environment. In addition to transcription, which directly regulate gene expression, accumulating evidence has showed that alternative splicing is also regulated by phytochromes. However, detailed mechanism is still not clear. Dr. Tu and his research group discovered that in moss Physcomitrella patens, phytochromes interact with a splicing regulator PphnRNP-F1 in a red light dependent manner. The interaction increases the protein level of PphnRNP-F1. Moreover, PphnRNP-F1 could be further recruited to the pre-mRNA by a GAA-repetitive, cis-regulatory element located on the exonic region to modulate alternative splicing. Their finding provides evidence to demonstrate a novel phytochrome-mediated signaling pathway for regulation of pre-mRNA splicing.

Shih et al., 2019, The Plant Cell

Alternative splicing is of importance to eukaryotic organisms, producing multiple mRNA isoforms from a single gene in response to environmental changes. Dr. Tu’s group discovered that in moss Physcomitrella patens, the red light photoreceptor phytochrome interacts with the splicing regulator PphnRNP-H1 in a red light dependent manner. Furthermore, PphnRNP-H1 associates with the PpPRP39-1, one of spliceosome components which functions in pre-mRNA splicing, to control splicing activities. Their results suggest that phytochromes target the early step of spliceosome assembly via a cascade of protein–protein interactions to control pre-mRNA splicing.

Taipei: 14:00-16:10, Monday, October 28th, 2019
Tainan: 14:00-15:30, Tuesday, October 29th, 2019

Taipei (October 28th): International Conference Lecture Hall, Humanities and Social Science Building, Academia Sinica, Taipei, Taiwan
Tainan (October 29th): Shang-Fa Yang Auditorium, Academia Sinica Biotechnology Center in Southern Taiwan

Professor Julia Bailey-Serres (UC MacArthur Foundation Chair|Director, Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Uiverside, USA)

Your attendance to the event will be cordially welcome.(No registration required)
For more information, please see the poster attached.

Wu et al., 2019 Molecular Plant Microbe Interactions

The bacterial type VI secretion system (T6SS) is an anti-bacterial and anti-host nanomachine deployed by many bacteria for bacterial competition and pathogenesis. Since ~25% of Gram(-) bacteria with sequenced genomes encode one to multiple T6SS gene clusters, these T6SS-harboring bacteria must evolve strategies to recognize their own kind from others during interbacterial interactions. The groups of Erh-Min Lai , Chih-Horng Kuo , and Jeff Chang (Oregon State University)  have established a collaboration and used members of plant pathogenic Agrobacterium tumefaciens to address this question.  By whole-genome sequencing, comparative genomic analyses, and large-scale pairwise interbacterial competition assays in planta, they discovered the importance of evolutionary lineage in interbacterial competition. The data showed that competing pairs at intra-genomospecies levels tended to exert only minor fitness costs regardless of effector-immunity incompatibility, while competing pairs at the inter-genomospecies level mostly exhibited antagonism. These results suggest that, beyond T6SS effector-immunity compatibility, the genetics of the competing strains also the environment in which they are competing can impact competition outcomes. This work is mainly contributed by 1st author Dr. Chih-Feng Wu, a former Ph.D. student/postdoc at Lai lab and currently a postdoc at Change lab and published in the journal Molecular Plant Microbe Interactions (Wu et al., 2019). This work was selected as the “editor pick” of the journal issue and highlighted by news release.


You-Yuan Pang *, Rita Jui-Hsien Lu* and Pao-Yang Chen (2019) Epigenomes

Epigenetic regulation plays an important role in gene regulation, and epigenetic markers such as DNA methylation and histone modifications are generally described as switches that regulate gene expression. Behavioral epigenetics is defined as the study of how epigenetic alterations induced by experience and environmental stress may affect animal behavior. It studies epigenetic alterations due to environmental enrichment. Generally, molecular processes underlying epigenetic regulation in behavioral epigenetics include DNA methylation, post-translational histone modifications, noncoding RNA activity, and other unknown molecular processes. Whether the inheritance of epigenetic features will occur is a crucial question. In general, the mechanism underlying inheritance can be explained by two main phenomena: germline-mediated epigenetic inheritance and interact epigenetic inheritance of somatic cells through germline. In this review, we focus on examining behavioral epigenetics based on its possible modes of inheritance and discuss the considerations in the research of epigenetic transgenerational inheritance.

* You-Yuan Pang is from IPMB Summer Undergraduate Internship Program.

You-Yuan Pang *, Rita Jui-Hsien Lu* and Pao-Yang Chen (2019) Epigenomes

Nature Plants

Coumarins are ubiquitously found in the plant kingdom and play important roles in plant defense and iron mobilization. Huei Hsuan Tsai, a TIGP student from Wolfgang Schmidt’s group who successfully defended her thesis last month, made significant contributions to a study that disproved the generally accepted model that the trans-cis isomerization and lactonization of o-hydroxycinnamoyl-CoAs to coumarins occur solely spontaneously, and showed that the biosynthesis of coumarins in roots is mediated enzymatically, which is particularly important under conditions of low iron availability.

In collaboration with Wout Boerjan’s group at VIB in Ghent, the IPMB researchers found that mutants defective in COUMARIN SYNTHASE (COSY), a newly identified enzyme in the phenylpropanoid pathway, have reduced iron content and show growth defects under conditions of low iron availability (Nature Plants). Recombinant COSY is able to produce umbelliferone, esculetin, and scopoletin from their respective o-hydroxycinnamoyl-CoA thioesters via two reaction steps: a trans-cis isomerization followed by a lactonization. This conversion happens partially spontaneously and is catalyzed by light, which explains why the need for an enzyme for this conversion has been overlooked. Because of its importance in iron uptake and plant defense, the discovery of COSY will potentially facilitate the development of crops with increased iron uptake and pest resistance, for instance via biotechnological engineering or marker-assisted breeding. Consistent with a conserved role in coumarin biosynthesis, orthologues of COSY are present in a wide range of plant species.

Nature Plants :https://doi.org/10.1038/s41477-019-0510-0

November 13 (Wed), 2019

A134, Agricultural Technology Building, Academia Sinica

Contact Person:
Ms. Hsiao-Yun Wang, 02-27871011,

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Chen et al., 2019, Scientific Reports.

The Orchidaceae is the largest and most diverse family of flowering plants. Because of the fascinating array of colors, delicate flower shapes, and fragrant blooms, orchids have become popular and valuable ornamental plants in the market. Taxonomically distinct Cymbidium mosaic potexvirus (CymMV) and Odontoglossum ringspot tobamovirus (ORSV) are two of the most prevalent viruses worldwide; when co-infecting orchids, they cause synergistic symptoms. Because of the huge economic loss in quality and quantity in the orchid industry with virus-infected orchids, virus-resistant orchids are urgently needed. To date, no transgenic resistant lines against these two viruses have been reported. Dr. Na-Sheng Lin’s group generated transgenic Nicotiana benthamiana expressing various constructs of partial CymMV and ORSV genomes. Several transgenic lines grew normally and remained symptomless after mixed inoculation with CymMV and ORSV. The replication of CymMV and ORSV was approximately 70% - 90% lower in protoplasts of transgenic lines than wild-type (WT) plants. Of note, extremely low or no viral RNA or capsid protein of CymMV and ORSV was detected in systemic leaves of transgenic lines after co-infection. Grafting experiments further revealed that CymMV and ORSV trafficked extremely inefficiently from co-infected WT stocks to transgenic scions, presumably due to RNA-mediated interference. This study reports the first successful creation of dual resistant transgenic lines against CymMV and ORSV and shed light on the commercial development of transgenic orchid production to combat the global viral threat. The article was reported in “Scientific Reports. 2019. 9:10230.” https://doi.org/10.1038/s41598-019-46695-7.