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Histone deacetylase Hos2 regulates protein expression noise by potentially modulating the protein translation machinery

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Nucleic Acids Research 2024年第13期52卷 7556-7571页

作者： Lin, Wei-Han Opoc, Florica J.G. Liao, Chia-Wei Roy, Kevin R. Steinmetz, Lars M. Leu, Jun-Yi Doctoral Program in Microbial Genomics National Chung Hsing University and Academia Sinica Institute of Molecular Biology Academia Sinica Stanford Genome Technology Center Stanford University Department of Genetics Stanford University School of Medicine European Molecular Biology Laboratory (EMBL) Genome Biology Unit

Non-genetic variations derived from expression noise at transcript or protein levels can result in cell-to-cell heterogeneity within an isogenic population. Although cells have developed strategies to reduce noise in some cellular functions, this heterogeneity can also facilitate varying levels of regulation and provide evolutionary benefits in specific environments. Despite several general characteristics of cellular noise having been revealed, the detailed molecular pathways underlying noise regulation remain elusive. Here, we established a dual-fluorescent reporter system in Saccharomyces cerevisiae and performed experimental evolution to search for mutations that increase expression noise. By analyzing evolved cells using bulk segregant analysis coupled with whole-genome sequencing, we identified the histone deacetylase Hos2 as a negative noise regulator. A hos2 mutant down-regulated multiple ribosomal protein genes and exhibited partially compromised protein translation, indicating that Hos2 may regulate protein expression noise by modulating the translation machinery. Treating cells with translation inhibitors or introducing mutations into several Hos2-regulated ribosomal protein genes—RPS9A, RPS28B and RPL42A—enhanced protein expression noise. Our study provides an effective strategy for identifying noise regulators and also sheds light on how cells regulate non-genetic variation through protein translation. © The Author(s) 2024.

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Hydrolysis of Gluten-Derived Celiac Disease-Triggering Peptides across a Broad pH Range by RmuAP1: A Novel Aspartic Peptidase Isolated from Rhodotorula mucilaginosa

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Journal of Agricultural and Food Chemistry 2023年第45期71卷 17202-17213页

作者： Zhang, Yu-Han Leu, Wei-Ming Meng, Menghsiao Ph.D. Program in Microbial Genomics National Chung Hsing University 250 Kuo-Kuang Road Taichung40227 Taiwan Academia Sinica 128 Academia Road Section 2 Taipei Nankang11529 Taiwan Graduate Institute of Biotechnology National Chung Hsing University 250 Kuo-Kuang Road Taichung40227 Taiwan

An aspartate peptidase with proteolytic activity toward gluten was identified from an isolated red yeast Rhodotorula mucilaginosa strain. This peptidase consists of 425 amino acids, comprising an N-terminal signal peptide, a propeptide, and a C-terminal catalytic domain. The catalytic domain, termed RmuAP1CD, could be secreted by the recombinant oleaginous yeast Yarrowia lipolytica, whose genome contains the expression cassette for RmuAP1CD. RmuAP1CD exhibited optimum activity at pH 2.5 when acting on bovine serum albumin. Moreover, it facilitated the hydrolysis of gluten-derived immunogenic peptides (GIPs), which are responsible for triggering celiac disease symptoms, across a pH range of 3.0-6.0. The preferred cleavage sites are P-Q-Q-↓-P-Q in the 26-mer and P-Q-L-↓-P-Y in the 33-mer GIPs. Conversely, porcine pepsin cannot hydrolyze these two GIPs. The ability of RmuAP1CD to degrade GIPs under acidic conditions of the stomach indicates its potential as a viable oral enzyme therapy for celiac disease. © 2023 The Authors. Published by American Chemical Society.

关键词： Peptides

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Development of a tag-free plant-made interferon gamma production system with improved therapeutic efficacy against viruses

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Frontiers in Bioengineering and Biotechnology 2023年 11卷 1341340页

作者： Jiang, Min-Chao Hsu, Wei-Li Tseng, Ching-Yu Lin, Na-Sheng Hsu, Yau-Heiu Hu, Chung-Chi PhD Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung Taiwan Institute of Plant and Microbial Biology Academia Sinica Taipei Taiwan Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan Advanced Plant Biotechnology Center National Chung Hsing University Taichung Taiwan

Plants offer a promising platform for cost-effective production of biologically active therapeutic glycoproteins. In previous studies, we have developed a plant expression system based on Bamboo mosaic virus (BaMV) by incorporating secretory signals and an affinity tag, which resulted in notably enhanced yields of soluble and secreted fusion glycoproteins (FGs) in Nicotiana benthamiana. However, the presence of fusion tags on recombinant glycoproteins is undesirable for biomedical applications. This study aimed to develop a refined expression system that can efficiently produce tag-free glycoproteins in plants, with enhanced efficacy of mature interferon gamma (mIFNγ) against viruses. To accommodate the specific requirement of different target proteins, three enzymatically or chemically cleavable linkers were provided in this renovated BaMV-based expression system. We demonstrated that Tobacco etch virus (TEV) protease could process the specific cleavage site (LTEV) of the fusion protein, designated as SSExtHis(SP)10LTEV-mIFNγ, with optimal efficiency under biocompatible conditions to generate tag-free mIFNγ glycoproteins. The TEV protease and secretory-affinity tag could be effectively removed from the target mIFNγ glycoproteins through Ni2+-NTA chromatography. In addition, the result of an antiviral assay showed that the tag-free mIFNγ glycoproteins exhibited enhanced biological properties against Sindbis virus, with comparable antiviral activity of the commercialized HEK293-expressed hIFNγ. Thus, the improved BaMV-based expression system developed in this study may provide an alternative strategy for producing tag-free therapeutic glycoproteins intended for biomedical applications. Copyright © 2024 Jiang, Hsu, Tseng, Lin, Hsu and Hu.

关键词： Glycoproteins

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Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller-size coral reef zooplankton by metatranscriptomics

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Molecular Ecology Resources 2024年第3期24卷 e13911-e13911页

作者： Mattos, Felipe M. G. Dreyer, Niklas Fong, Chia-Ling Wen, Yung-Hui Victoria Jain, Dharmesh De Vivo, Mattia Huang, Yu-Sin Mwihaki, John Karichu Wang, Tzi-Yuan Ho, Ming-Jay Tsai, Isheng Jason Wang, John Chan, Benny K. K. Machida, Ryuji J. Biodiversity Research Center Academia Sinica Taipei Taiwan Department of Life Science National Taiwan Normal University Taipei Taiwan Biodiversity Program Taiwan International Graduate Program Academia Sinica and National Taiwan Normal University Taipei Taiwan Natural History Museum of Denmark Invertebrate Zoology University of Copenhagen Copenhagen Denmark Institute of Plant and Microbial Biology Academia Sinica Taipei Taiwan Ph.D. Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taipei Taiwan Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan Molecular and Biological Agricultural Sciences Taiwan International Graduate Program Academia Sinica and National Chung Hsing University Taipei Taiwan

PCR-based high-throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR-based approaches. Marine drifting animals—zooplankton—play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans and others. In the present study, we collected 48 size-fractionated zooplankton samples in the vicinity of a coral reef island with environmental gradients. To investigate the spatiotemporal dynamics of zooplankton diversity patterns and the effect of PCR amplification biases across these complex communities, we first took metatranscriptomics approach. Comprehensive computational analyses revealed a clear pattern of higher/lower homogeneity in smaller/larger zooplankton compositions across samples respectively. Our study thus suggests changes in the role of dispersal across the sizes. Next, we applied in silico PCR to the metatranscriptomics datasets, in order to estimate the extent of PCR amplification bias. Irrespective of stringency criteria, we observed clear separations of size fraction sample clusters in both metatranscriptomics and in silico datasets. In contrast, the pattern—smaller-fractioned communities had higher compositional homogeneity than larger ones—was observed in the metatranscriptomics data but not in the in silico datasets. To investigate this discrepancy further, we analysed the mismatches of widely used mitochondrial CO1 primers and identified priming site mismatches likely driving PCR-based biases. Our results suggest the use of metatranscriptomics or, although less ideal, redesigning the CO1 primers is necessary to circumvent these issues. © 2023 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.

关键词： coral reef diversity in silico PCR metatranscriptomics size fraction zooplankton

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MEF2C regulates osteoclastogenesis and pathologic bone resorption via c-FOS

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Bone Research 2021年第1期9卷 50-62页

作者： Takayuki Fujii Koichi Murata Se-Hwan Mun Seyeon Bae Ye Ji Lee Tannia Pannellini Kyuho Kang David Oliver Kyung-Hyun Park-Min Lionel B.Ivashkiv Arthritis and Tissue Degeneration Program and David Z.Rosensweig Genomics Research Center Hospital for Special SurgeryNew YorkNY 10021USA Department of Orthopaedic Surgery Kyoto University Graduate School of MedicineSakyoKyoto 606-8507Japan Department of Advanced Medicine for Rheumatic Diseases Kyoto University Graduate School of MedicineSakyoKyoto 606-8507Japan Department of Biology Chungbuk National UniversityCheongju 28644Republic of Korea BCMB Allied Program Weill Cornell Graduate School of Medical ScienceNew YorkNY 10021USA Immunology and Microbial Pathogenesis Program Weill Cornell Graduate School of Medical ScienceNew YorkNY 10021USA

Osteoporosis is a metabolic bone disease with dysregulated coupling between bone resorption and bone formation,which results in decreased bone mineral *** MEF2C locus,which encodes the transcription factor MADS box transcription enhancer factor 2,polypeptide C(MEF2C),is strongly associated with adult osteoporosis and osteoporotic *** the role of MEF2C in bone and cartilage formation by osteoblasts,osteocytes,and chondrocytes has been studied,the role of MEF2C in osteoclasts,which mediate bone resorption,remains *** this study,we identified MEF2C as a positive regulator of human and mouse osteoclast *** decreased MEF2C expression resulted in diminished osteoclastogenesis,ectopic expression of MEF2C enhanced osteoclast *** transcriptomic and bioinformatic approaches,we found that MEF2C promotes the RANKL-mediated induction of the transcription factors c-FOS and NFATc1,which play a key role in ***,MEF2C binds to FOS regulatory regions to induce c-FOS expression,leading to the activation of NFATC1 and downstream *** deletion of Mef2c in mice resulted in increased bone mass under physiological conditions and protected mice from bone erosion by diminishing osteoclast formation in K/BxN serum induced arthritis,a murine model of inflammatory *** findings reveal direct regulation of osteoclasts by MEF2C,thus adding osteoclasts as a cell type in which altered MEF2C expression or function can contribute to pathological bone remodeling.

关键词： osteoclast MEF2C pathologic

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Essential oil extracted from Hirami lemon (Citrus reticulata var. depressa) agricultural waste promotes mitochondrial biogenesis in C₂C₁₂ skeletal muscle cells

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NFS Journal 2025年 39卷

作者： Wang, Chung-Hsuan Yeo, Ying-Hao Lin, Chia-Hsin Xu, Mo-rong Wang, Sheng-Yang Special Crop and Metabolome Discipline Cluster Academy Circle Economy National Chung Hsing University Taichung 40227 Taiwan Department of Forestry National Chung Hsing University Taichung 402 Taiwan Doctoral Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung 402 Taiwan Agricultural Biotechnology Research Center Academia Sinica Taipei 108 Taiwan

With increasing awareness of the circular economy, extracting valuable components from agricultural waste offers opportunities to create high-value products. Citrus reticulata var. depressa (CD), endemic to Taiwan, produces sour fruits mainly for juice, leaving significant peel waste. In this study, we extract essential oil (CDEO) from CD peels and examines its effects on skeletal muscle energy metabolism. ATP measurements and mitochondrial staining show that CDEO enhances ATP content, mitochondrial membrane potential, and mass in C₂C₁₂ cells. RT-PCR and Western blot analyses indicate that CDEO activates the p-AMPK/SIRT1/PGC-1α pathway and upregulates Nrf1, Nrf2, and TFAM expression. Among the identified constituents, γ-terpinene was found to be the major bioactive compound, capable of promoting ATP production and mitochondrial biogenesis. Future studies should further investigate mitochondrial function and evaluate its anti-fatigue potential using in vivo models. © 2025 The Authors

关键词： Agricultural waste Anti-fatigue ATP Citrus reticulata var. depressa Essential oil

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Argonaute 5-mediated antiviral defense and viral counter-defense in Nicotiana benthamiana

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Virus Research 2023年第1期334卷 199179页

作者： Tu, Chin-Wei Huang, Ying-Wen Lee, Chin-Wei Kuo, Song-Yi Lin, Na-Sheng Hsu, Yau-Heiu Hu, Chung-Chi PhD Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung 40227 Taiwan Graduate Institute of Biotechnology National Chung Hsing University Taichung 40227 Taiwan Advanced Plant Biotechnology Center National Chung Hsing University Taichung 40227 Taiwan Temasek Life Sciences Laboratory National University of Singapore Singapore 117604 Singapore Institute of Plant and Microbial Biology Academia Sinica Taipei 11529 Taiwan

The argonaute (AGO) family proteins play a crucial role in preventing viral invasions through the plant antiviral RNA silencing pathway, with distinct AGO proteins recruited for specific antiviral mechanisms. Our previous study revealed that Nicotiana benthamiana AGO5 (NbAGO5) expression was significantly upregulated in response to bamboo mosaic virus (BaMV) infection. However, the roles of NbAGO5 in antiviral mechanisms remained to be explored. In this research, we examined the antiviral functions of NbAGO5 in the infections of different viruses. It was found that the accumulation of NbAGO5 was induced not only at the RNA but also at the protein level following the infections of BaMV, potato virus X (PVX), tobacco mosaic virus (TMV), and cucumber mosaic virus (CMV) in N. benthamiana. To explore the antiviral mechanism and regulatory function of NbAGO5, we generated NbAGO5 overexpression (OE-NbAGO5) and knockout (nbago5) transgenic N. benthamiana lines. Our findings reveal that NbAGO5 provides defense against BaMV, PVX, TMV, and a mutant CMV deficient in 2b gene, but not against the wild-type CMV and turnip mosaic virus (TuMV). Through affinity purification and small RNA northern blotting, we demonstrated that NbAGO5 exerts its antiviral function by binding to viral small interfering RNAs (vsiRNAs). Moreover, we observed that CMV 2b and TuMV HC-Pro interact with NbAGO5, triggering its degradation via the 26S proteasome and autophagy pathways, thereby allowing these viruses to overcome NbAGO5-mediated defense. In addition, TuMV HC-Pro provides another line of counter-defense by interfering with vsiRNA binding by NbAGO5. Our study provides further insights into the antiviral RNA interference mechanism and the complex interplay between NbAGO5 and plant viruses. © 2023

关键词： 26S proteasome AGO5 Autophagy Plant antiviral defense RNA silencing Viral suppressors of RNA silencing (VSR)

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Gn protein expressed in plants for diagnosis of severe fever with thrombocytopenia syndrome virus

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Applied Microbiology and Biotechnology 2024年第1期108卷 303-303页

作者： Chang, Yu-Chih Shimoda, Hiroshi Jiang, Min-Chao Hsu, Yau-Heiu Maeda, Ken Yamada, Yumiko Hsu, Wei-Li Doctoral Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung Taiwan Laboratory of Veterinary Microbiology Joint Faculty of Veterinary Medicine Yamaguchi University Yamaguchi Japan Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan Department of Veterinary Science National Institute of Infectious Disease Tokyo Japan The iEGG and Animal Biotechnology Center National Chung Hsing University Taichung402 Taiwan

Abstract: Severe fever with thrombocytopenia syndrome virus (SFTSV) causes the highly fatal disease in humans. To facilitate diagnosis, the native form of subunit glycoprotein (Gn), a prime target for potential vaccines and therapies, was produced in Nicotiana benthamiana using a Bamboo mosaic virus-based vector system. By fusion with secretory signal tags, SSExt, derived from the extension protein, and the (SP)10 motif, the yield of the recombinant Gn (rGn) was remarkably increased to approximately 7 mg/kg infiltrated leaves. Ultimately, an rGn-based ELISA was successfully established for the detection of SFTSV-specific antibodies in serum samples from naturally infected monkeys. As validated with the reference method, the specificity and sensitivity of rGn-ELISA were 94% and 96%, respectively. In conclusion, utilizing well-suited fusion tags facilitates rGn production and purification in substantial quantities while preserving its antigenic properties. The rGn-ELISA, characterized by its commendable sensitivity and specificity could serve as a viable alternative diagnostic method for assessing SFTSV seroprevalence. Key points: • SFTSV Gn, fused with secretory signal tags, was expressed by the BaMV-based vector. • The plant fusion tags increased expression levels and eased the purification of rGn. • The rGn-ELISA was established and validated;its specificity and sensitivity > 94%. © The Author(s) 2024.

关键词： Glycoproteins

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First report of a 16SrII-A subgroup ‘Candidatus Phytoplasma aurantifolia’-related strain associated with Celosia argentea in Taiwan

New Disease Reports

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New Disease Reports 2023年第2期48卷

作者： Mejia, H.M. Chiu, Y.-C. Chen, Y.-K. Liao, P.-Q. Yang, J.-Y. Institute of Biochemistry National Chung Hsing University Taichung Taiwan Doctoral Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan Department of Plant Pathology National Chung Hsing University Taichung Taiwan Institute of Biotechnology National Chung Hsing University Taichung Taiwan Advanced Plant and Food Crop Biotechnology Center National Chung Hsing University Taichung Taiwan

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Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines

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细胞研究（英文版） 2021年第7期31卷 732-741页

作者： Yunlong Cao Ayijiang Yisimayi Yali Bai Weijin Huang Xiaofeng Li Zhiying Zhang Tianjiao Yuan Ran An Jing Wang Tianhe Xiao Shuo Du Wenping Ma Liyang Song Yongzheng Li Xiang Li Weiliang Song Jiajing Wu Shuo Liu Xuemei Li Yonghong Zhang Bin Su Xianghua Guo Yangyang Wei Chuanping Gao Nana Zhang Yifei Zhang Yang Dou Xiaoyu Xu Rui Shi Bai Lu Ronghua Jin Yingmin Ma Chengfeng Qin Youchun Wang Yingmei Feng Junyu Xiao Xiaoliang Sunney Xie Beijing Advanced Innovation Center for Genomics (ICG) Peking UniversityBeijingChina Biomedical Pioneering Innovation Center (BIOPIC) Peking UniversityBeijingChina Beijing Advanced Innovation Center for Genomics (ICG) Peking UniversityBeijingChina Biomedical Pioneering Innovation Center (BIOPIC) Peking UniversityBeijingChina School of Life Sciences Peking UniversityBeijingChina Beijing Advanced Innovation Center for Genomics (ICG) Peking UniversityBeijingChina Joint Graduate Program of Peking-Tsinghua-NIBS School of Life SciencesTsinghua UniversityBeijingChina Division of HIV/AIDS and Sex-transmitted Virus Vaccines Institute for Biological Product ControlNational Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of BiologicalsBeijingChina State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and EpidemiologyAcademy of Military Medical SciencesBeijingChina Beijing Advanced Innovation Center for Genomics (ICG) Peking UniversityBeijingChina School of Life Sciences Peking UniversityBeijingChina Beijing Advanced Innovation Center for Genomics (ICG) Peking UniversityBeijingChina Biomedical Pioneering Innovation Center (BIOPIC) Peking UniversityBeijingChina Peking-Tsinghua Center for life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina Beijing Youan Hospital Capital Medical UniversityBeijingChina Beijing Advanced Innovation Center for Genomics (ICG) Peking UniversityBeijingChina Peking-Tsinghua Center for life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina School of Pharmaceutical Sciences IDG/McGovern Institute for Brain ResearchTsinghua UniversityBeijingChina Vazyme Biotech Co. LtdNanjingJiangsuChina CAS Key Laboratory of Microbial Physiological and Metabolic Engineering Institute of MicrobiologyChinese Academy of SciencesBeijingChina Beijing Ditan Hospital Capital Medical UniversityBeijingChina

SARS-CoV-2 variants could induce immune escape by mutations on the receptor-binding domain (RBD) and N-terminal domain(NTD).Here we report the humoral immune response to circulating SARS-CoV-2 variants,such as 501Y.V2 (B.1.351),of the plasma and neutralizing antibodies (NAbs) elicited by CoronaVac (inactivated vaccine),ZF2001 (RBD-subunit vaccine) and natural *** 86 potent NAbs identified by high-throughput single-cell VDJ sequencing of peripheral blood mononuclear cells from vaccinees and convalescents,near half anti-RBD NAbs showed major neutralization reductions against the K417N/E484K/N501Y mutation combination,with E484K being the dominant ***3-53/VH3-66 recurrent antibodies respond differently to RBD variants,and K417N compromises the majority of neutralizing activity through reduced polar contacts with complementarity determining *** contrast,the 242-244 deletion (242-244A) would abolish most neutralization activity of anti-NTD NAbs by interrupting the conformation of NTD antigenic supersite,indicating a much less diversity of anti-NTD NAbs than anti-RBD *** of convalescents and CoronaVac vaccinees displayed comparable neutralization reductions against pseudo-and authentic 501Y.V2 variants,mainly caused by E484K/N501Y and 242-244△,with the effects being ***,RBD-subunit vaccinees exhibit markedly higher tolerance to 501Y.V2 than convalescents,since the elicited anti-RBD NAbs display a high diversity and are unaffected by NTD ***,an extended gap between the third and second doses of ZF2001 leads to better neutralizing activity and tolerance to 501Y.V2 than the standard three-dose ***,these results suggest that the deployment of RBD-vaccines,through a third-dose boost,may be ideal for combating SARS-CoV-2 variants when necessary,especially for those carrying mutations that disrupt the NTD supersite.

关键词： Cryoelectron microscopy Immunology X-ray crystallography

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