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Wu TY, Li YR, Chang KJ, Fang JC, Urano D, Liu MJ. Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes. Genome Res 2024; 34:272-285. [PMID: 38479836 PMCID: PMC10984385 DOI: 10.1101/gr.278100.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in the tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and nonAUG TISs in 5' untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots, and humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby cis-regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence of cis-regulatory signatures across plant species, humans, and viruses suggests their broad and critical roles in reprogramming the translational landscape.
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Affiliation(s)
- Ting-Ying Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Ya-Ru Li
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Kai-Jyun Chang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Jhen-Cheng Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan;
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
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2
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Lung SC, Tsou MM, Hu S, Hsieh Y, Wang WV, Shui C, Tan C. Concurrent assessment of personal, indoor, and outdoor PM 2.5 and PM 1 levels and source contributions using novel low-cost sensing devices. Indoor Air 2021; 31:755-768. [PMID: 33047373 PMCID: PMC8247015 DOI: 10.1111/ina.12763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
The intensity, frequency, duration, and contribution of distinct PM2.5 sources in Asian households have seldom been assessed; these are evaluated in this work with concurrent personal, indoor, and outdoor PM2.5 and PM1 monitoring using novel low-cost sensing (LCS) devices, AS-LUNG. GRIMM-comparable observations were acquired by the corrected AS-LUNG readings, with R2 up to 0.998. Twenty-six non-smoking healthy adults were recruited in Taiwan in 2018 for 7-day personal, home indoor, and home outdoor PM monitoring. The results showed 5-min PM2.5 and PM1 exposures of 11.2 ± 10.9 and 10.5 ± 9.8 µg/m3 , respectively. Cooking occurred most frequently; cooking with and without solid fuel contributed to high PM2.5 increments of 76.5 and 183.8 µg/m3 (1 min), respectively. Incense burning had the highest mean PM2.5 indoor/outdoor (1.44 ± 1.44) ratios at home and on average the highest 5-min PM2.5 increments (15.0 µg/m3 ) to indoor levels, among all single sources. Certain events accounted for 14.0%-39.6% of subjects' daily exposures. With the high resolution of AS-LUNG data and detailed time-activity diaries, the impacts of sources and ventilations were assessed in detail.
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Affiliation(s)
- Shih‐Chun Candice Lung
- Research Center for Environmental ChangesAcademia SinicaTaipeiTaiwan
- Department of Atmospheric SciencesNational Taiwan UniversityTaipeiTaiwan
- Institute of Environmental and Occupational Health SciencesNational Taiwan UniversityTaipeiTaiwan
| | | | - Shu‐Chuan Hu
- Research Center for Environmental ChangesAcademia SinicaTaipeiTaiwan
| | - Yu‐Hui Hsieh
- Research Center for Environmental ChangesAcademia SinicaTaipeiTaiwan
| | | | - Chen‐Kai Shui
- Research Center for Environmental ChangesAcademia SinicaTaipeiTaiwan
| | - Chee‐Hong Tan
- Research Center for Environmental ChangesAcademia SinicaTaipeiTaiwan
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3
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Li C, Liau ES, Lee Y, Huang Y, Liu Z, Willems A, Garside V, McGlinn E, Chen J, Hong T. MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback. Mol Syst Biol 2021; 17:e9945. [PMID: 33890404 PMCID: PMC8062999 DOI: 10.15252/msb.20209945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 11/09/2022] Open
Abstract
Positive feedback driven by transcriptional regulation has long been considered a key mechanism underlying cell lineage segregation during embryogenesis. Using the developing spinal cord as a paradigm, we found that canonical, transcription-driven feedback cannot explain robust lineage segregation of motor neuron subtypes marked by two cardinal factors, Hoxa5 and Hoxc8. We propose a feedback mechanism involving elementary microRNA-mRNA reaction circuits that differ from known feedback loop-like structures. Strikingly, we show that a wide range of biologically plausible post-transcriptional regulatory parameters are sufficient to generate bistable switches, a hallmark of positive feedback. Through mathematical analysis, we explain intuitively the hidden source of this feedback. Using embryonic stem cell differentiation and mouse genetics, we corroborate that microRNA-mRNA circuits govern tissue boundaries and hysteresis upon motor neuron differentiation with respect to transient morphogen signals. Our findings reveal a previously underappreciated feedback mechanism that may have widespread functions in cell fate decisions and tissue patterning.
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Affiliation(s)
- Chung‐Jung Li
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia Sinica and Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Ee Shan Liau
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia Sinica and Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Yi‐Han Lee
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Yang‐Zhe Huang
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Ziyi Liu
- Genome Science and Technology ProgramThe University of TennesseeKnoxvilleTNUSA
| | - Andrew Willems
- Genome Science and Technology ProgramThe University of TennesseeKnoxvilleTNUSA
| | - Victoria Garside
- EMBL AustraliaAustralian Regenerative Medicine InstituteMonash UniversityClaytonVicAustralia
| | - Edwina McGlinn
- EMBL AustraliaAustralian Regenerative Medicine InstituteMonash UniversityClaytonVicAustralia
| | - Jun‐An Chen
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia Sinica and Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
- Neuroscience Program Academia SinicaTaipeiTaiwan
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular BiologyThe University of TennesseeKnoxvilleTNUSA
- National Institute for Mathematical and Biological SynthesisKnoxvilleTNUSA
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4
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Abstract
BACKGROUND Endometriosis is a common gynecological condition in which stromal or glandular epithelium is implanted in extrauterine locations. Endometriosis causes detrimental effects on the granulosa cells, and phthalate interferes with the biological and reproductive function of endometrial cells at a molecular level. METHODS This article retrospectively reviewed the studies on phthalate exposure and its relationship with endometriosis. A literature search was performed for scientific articles using the keywords "phthalate and endometriosis," "endometriosis and granulosa cells," "phthalate and granulosa cells," and "phthalates and endometrial cells." RESULTS Endometriosis can affect cytokine production, steroidogenesis, cell cycle progression, expression of estrogen receptor-α (ER-α)/progesterone receptor (PR), and cause endoplasmic reticulum stress, senescence, apoptosis, autophagy, and oxidative stress in the granulosa cells. Mono-n-butyl phthalate (MnBP) alters the expression of cytokines, cell cycle-associated genes, ovarian stimulation, steroidogenesis, and progesterone production. Several in vitro studies have demonstrated that phthalate caused inflammation, invasion, change in cytokines, increased oxidative stress, viability, resistance to hydrogen peroxide, and proliferation of endometrial cells. CONCLUSION This might provide new insights about the impact of phthalate on the pathogenesis of endometriosis and its consequences on the ovarian function.
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Affiliation(s)
- Ya‐Ching Chou
- Department of Biological Science and TechnologyCollege of Biological Science and TechnologyNational Chiao Tung UniversityHsinchuTaiwan
- Center for Intelligent Drug Systems and Smart Bio‐devices (IDSB)National Chiao Tung UniversityHsinchuTaiwan
| | - Chii‐Ruey Tzeng
- Department of Obstetrics and GynecologyTaipei Medical UniversityTaipeiTaiwan
- Taipei Fertility Center, TaipeiTaiwan
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Chang C, Huang H, Tsai H, Lin S, Liu P, Chen W, Hsu F, Nie W, Chen Y, Wang L. Facile Fabrication of Self-Assembly Functionalized Polythiophene Hole Transporting Layer for High Performance Perovskite Solar Cells. Adv Sci (Weinh) 2021; 8:2002718. [PMID: 33717841 PMCID: PMC7927620 DOI: 10.1002/advs.202002718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Crystallinity and crystal orientation have a predominant impact on a materials' semiconducting properties, thus it is essential to manipulate the microstructure arrangements for desired semiconducting device performance. Here, ultra-uniform hole-transporting material (HTM) by self-assembling COOH-functionalized P3HT (P3HT-COOH) is fabricated, on which near single crystal quality perovskite thin film can be grown. In particular, the self-assembly approach facilitates the P3HT-COOH molecules to form an ordered and homogeneous monolayer on top of the indium tin oxide (ITO) electrode facilitate the perovskite crystalline film growth with high quality and preferred orientations. After detailed spectroscopy and device characterizations, it is found that the carboxylic acid anchoring groups can down-shift the work function and passivate the ITO surface, retarding the interface carrier recombination. As a result, the device made with the self-assembled HTM show high open-circuit voltage over 1.10 V and extend the lifetime over 4,300 h when storing at 30% relative humidity. Moreover, the cell works efficiently under much reduced light power, making it useful as power source under dim-light conditions. The demonstration suggests a new facile way of fabricating monolayer HTM for high efficiency perovskite devices, as well as the interconnecting layer needed for tandem cell.
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Affiliation(s)
- Chi‐Yuan Chang
- Center for Condensed Matter SciencesNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
- Department of PhysicsNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
| | - Hsin‐Hsiang Huang
- Center for Condensed Matter SciencesNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
- Materials Science Division and Center for Molecular EngineeringArgonne National LaboratoryLemontIL60439USA
- Department of Material Science and EngineeringNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
| | - Hsinhan Tsai
- Center for Integrated Nanotechnologies, Materials Physics and Application DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Shu‐Ling Lin
- Center for Condensed Matter SciencesNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
| | - Pang‐Hsiao Liu
- Center for Condensed Matter SciencesNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
- Department of Material Science and EngineeringNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
| | - Wei Chen
- Materials Science Division and Center for Molecular EngineeringArgonne National LaboratoryLemontIL60439USA
- Pritzker School of Molecular EngineeringUniversity of ChicagoChicagoIL60637USA
| | - Fang‐Chi Hsu
- Department of Material Science and EngineeringNational United University1, LiendaMiaoli36003Taiwan
| | - Wanyi Nie
- Center for Integrated Nanotechnologies, Materials Physics and Application DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Yang‐Fang Chen
- Center for Condensed Matter SciencesNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
- Department of PhysicsNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
| | - Leeyih Wang
- Center for Condensed Matter SciencesNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
- Institute of Polymer Science and EngineeringNational Taiwan UniversityNo. 1, Sec. 4, Roosevelt Rd.Taipei10617Taiwan
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6
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Hsieh P, Chung Y, Lee K, Wang S, Lu C, Hsieh M. The rice PALE1 homolog is involved in the biosynthesis of vitamin B1. Plant Biotechnol J 2021; 19:218-220. [PMID: 32777168 PMCID: PMC7868968 DOI: 10.1111/pbi.13465] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 07/10/2020] [Accepted: 08/02/2020] [Indexed: 05/04/2023]
Affiliation(s)
- Ping‐Han Hsieh
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Yi‐Hsin Chung
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Kim‐Teng Lee
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Shi‐Yun Wang
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Chung‐An Lu
- Department of Life SciencesNational Central UniversityTaoyuanTaiwan
| | - Ming‐Hsiun Hsieh
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
- Department of Life SciencesNational Central UniversityTaoyuanTaiwan
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7
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Huang K, Lin M, Kuo T, Chen C, Lin C, Chou Y, Chao T, Pang Y, Kao H, Huang R, Lin S, Chang S, Yang P. Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. EMBO Mol Med 2021; 13:e12828. [PMID: 33159417 PMCID: PMC7799362 DOI: 10.15252/emmm.202012828] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 12/17/2022] Open
Abstract
To circumvent the devastating pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, a humanized decoy antibody (ACE2-Fc fusion protein) was designed to target the interaction between viral spike protein and its cellular receptor, angiotensin-converting enzyme 2 (ACE2). First, we demonstrated that ACE2-Fc could specifically abrogate virus replication by blocking the entry of SARS-CoV-2 spike-expressing pseudotyped virus into both ACE2-expressing lung cells and lung organoids. The impairment of viral entry was not affected by virus variants, since efficient inhibition was also observed in six SARS-CoV-2 clinical strains, including the D614G variants which have been shown to exhibit increased infectivity. The preservation of peptidase activity also enables ACE2-Fc to reduce the angiotensin II-mediated cytokine cascade. Furthermore, this Fc domain of ACE2-Fc was shown to activate NK cell degranulation after co-incubation with Spike-expressing H1975 cells. These promising characteristics potentiate the therapeutic prospects of ACE2-Fc as an effective treatment for COVID-19.
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Affiliation(s)
- Kuo‐Yen Huang
- Institute of Biomedical SciencesAcademia SinicaTaipeiTaiwan
| | - Ming‐Shiu Lin
- Institute of Biomedical SciencesAcademia SinicaTaipeiTaiwan
| | - Ting‐Chun Kuo
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Ci‐Ling Chen
- Institute of Biomedical SciencesAcademia SinicaTaipeiTaiwan
| | - Chung‐Chih Lin
- Institute of Biomedical SciencesAcademia SinicaTaipeiTaiwan
| | - Yu‐Chi Chou
- Biomedical Translation Research Center (BioTReC)Academia SinicaTaipeiTaiwan
| | - Tai‐Ling Chao
- Department of Clinical Laboratory Sciences and Medical BiotechnologyNational Taiwan University College of MedicineTaipeiTaiwan
| | - Yu‐Hao Pang
- Department of Clinical Laboratory Sciences and Medical BiotechnologyNational Taiwan University College of MedicineTaipeiTaiwan
| | - Han‐Chieh Kao
- Department of Clinical Laboratory Sciences and Medical BiotechnologyNational Taiwan University College of MedicineTaipeiTaiwan
| | - Rih‐Sheng Huang
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
| | - Steven Lin
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
| | - Sui‐Yuan Chang
- Department of Clinical Laboratory Sciences and Medical BiotechnologyNational Taiwan University College of MedicineTaipeiTaiwan
- Department of Laboratory MedicineNational Taiwan University HospitalTaipeiTaiwan
| | - Pan‐Chyr Yang
- Institute of Biomedical SciencesAcademia SinicaTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
- Genomics Research CenterAcademia SinicaTaipeiTaiwan
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8
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Yu C, Lin Y, Li H. Increased ratio of galactolipid MGDG : DGDG induces jasmonic acid overproduction and changes chloroplast shape. New Phytol 2020; 228:1327-1335. [PMID: 32585752 PMCID: PMC7689733 DOI: 10.1111/nph.16766] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 06/14/2020] [Indexed: 05/11/2023]
Abstract
Galactolipids monogalactosyl diacylglycerol (MGDG) and digalactosyl diacylglycerol (DGDG) constitute c. 50% and c. 30% of chloroplast membrane lipids, respectively. They are important for photosynthesis and stress tolerance. Mutations in DGD1, the major DGDG-synthesizing enzyme, severely reduce DGDG content and induce jasmonic acid (JA) overproduction, resulting in stunted growth. However, how DGDG reduction leads to JA overproduction is unknown. We introduced an inducible microRNA (ami-MGD1) into an Arabidopsis dgd1 mutant to reduce MGDG synthesis, thereby further diminishing galactolipid content, but partially restoring the MGDG : DGDG ratio. Galactolipid and Chl contents, expression of JA-biosynthesis and JA-responsive genes, photosystem II (PSII) maximum quantum efficiency, and chloroplast shape were investigated. Expression of JA-biosynthesis and JA-responsive genes were reduced in amiR-MGD1-transformed dgd1 plants. Stunted growth caused by JA overproduction was also partially rescued, but Chl reduction and PSII impairment remained similar to the original dgd1 mutant. Altered chloroplast shape, which is another defect observed in dgd1 but is not caused by JA overproduction, was also partially rescued. Our results reveal that an increased MGDG : DGDG ratio is the primary cause of JA overproduction. The ratio is also important for determining chloroplast shapes, whereas reduced Chl and photosynthesis are most likely a direct consequence of insufficient DGDG.
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Affiliation(s)
- Chun‐Wei Yu
- Institute of Molecular BiologyAcademia SinicaTaipei11529Taiwan
| | - Yang‐Tsung Lin
- Institute of Molecular BiologyAcademia SinicaTaipei11529Taiwan
| | - Hsou‐min Li
- Institute of Molecular BiologyAcademia SinicaTaipei11529Taiwan
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9
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Wu AY, Sung Y, Chen Y, Chou ST, Guo V, Chien JC, Ko JJ, Yang AL, Huang H, Chuang J, Wu S, Ho M, Ericsson M, Lin W, Cheung CHY, Juan H, Ueda K, Chen Y, Lai CP. Multiresolution Imaging Using Bioluminescence Resonance Energy Transfer Identifies Distinct Biodistribution Profiles of Extracellular Vesicles and Exomeres with Redirected Tropism. Adv Sci (Weinh) 2020; 7:2001467. [PMID: 33042758 PMCID: PMC7539214 DOI: 10.1002/advs.202001467] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/10/2020] [Indexed: 05/10/2023]
Abstract
Extracellular particles (EPs) including extracellular vesicles (EVs) and exomeres play significant roles in diseases and therapeutic applications. However, their spatiotemporal dynamics in vivo have remained largely unresolved in detail due to the lack of a suitable method. Therefore, a bioluminescence resonance energy transfer (BRET)-based reporter, PalmGRET, is created to enable pan-EP labeling ranging from exomeres (<50 nm) to small (<200 nm) and medium and large (>200 nm) EVs. PalmGRET emits robust, sustained signals and allows the visualization, tracking, and quantification of the EPs from whole animal to nanoscopic resolutions under different imaging modalities, including bioluminescence, BRET, and fluorescence. Using PalmGRET, it is shown that EPs released by lung metastatic hepatocellular carcinoma (HCC) exhibit lung tropism with varying distributions to other major organs in immunocompetent mice. It is further demonstrated that gene knockdown of lung-tropic membrane proteins, solute carrier organic anion transporter family member 2A1, alanine aminopeptidase/Cd13, and chloride intracellular channel 1 decreases HCC-EP distribution to the lungs and yields distinct biodistribution profiles. It is anticipated that EP-specific imaging, quantitative assays, and detailed in vivo characterization are a starting point for more accurate and comprehensive in vivo models of EP biology and therapeutic design.
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Affiliation(s)
- Anthony Yan‐Tang Wu
- Institute of Atomic and Molecular SciencesAcademia SinicaTaipei10617Taiwan
- Department of Pharmacology, College of MedicineNational Taiwan UniversityTaipei100233Taiwan
- Chemical Biology and Molecular Biophysics ProgramTaiwan International Graduate ProgramAcademia SinicaTaipei11529Taiwan
| | - Yun‐Chieh Sung
- Institute of Biomedical Engineering and Frontier Research Center on Fundamental and Applied Sciences of MattersNational Tsing Hua UniversityHsinchu30013Taiwan
- Department of Chemical EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Yen‐Ju Chen
- Institute of Atomic and Molecular SciencesAcademia SinicaTaipei10617Taiwan
| | | | - Vanessa Guo
- Institute of Atomic and Molecular SciencesAcademia SinicaTaipei10617Taiwan
| | | | - John Jun‐Sheng Ko
- Institute of Atomic and Molecular SciencesAcademia SinicaTaipei10617Taiwan
| | - Alan Ling Yang
- Institute of Atomic and Molecular SciencesAcademia SinicaTaipei10617Taiwan
| | - Hsi‐Chien Huang
- Institute of Biomedical Engineering and Frontier Research Center on Fundamental and Applied Sciences of MattersNational Tsing Hua UniversityHsinchu30013Taiwan
- Department of Chemical EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Ju‐Chen Chuang
- Institute of Atomic and Molecular SciencesAcademia SinicaTaipei10617Taiwan
| | - Syuan Wu
- Institute of Atomic and Molecular SciencesAcademia SinicaTaipei10617Taiwan
| | - Meng‐Ru Ho
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Maria Ericsson
- Department of Cell BiologyHarvard Medical SchoolBostonMA02115USA
| | - Wan‐Wan Lin
- Department of Pharmacology, College of MedicineNational Taiwan UniversityTaipei100233Taiwan
| | | | - Hsueh‐Fen Juan
- Department of Life ScienceNational Taiwan UniversityTaipei10617Taiwan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyo135‐8550Japan
| | - Yunching Chen
- Institute of Biomedical Engineering and Frontier Research Center on Fundamental and Applied Sciences of MattersNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Charles Pin‐Kuang Lai
- Institute of Atomic and Molecular SciencesAcademia SinicaTaipei10617Taiwan
- Chemical Biology and Molecular Biophysics ProgramTaiwan International Graduate ProgramAcademia SinicaTaipei11529Taiwan
- Genome and Systems Biology Degree ProgramNational Taiwan University and Academia SinicaTaipei10617Taiwan
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10
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Lo S, Cheng M, Hsing YC, Chen Y, Lee K, Hong Y, Hsiao Y, Hsiao A, Chen P, Wong L, Chen N, Reuzeau C, Ho TD, Yu S. Rice Big Grain 1 promotes cell division to enhance organ development, stress tolerance and grain yield. Plant Biotechnol J 2020; 18:1969-1983. [PMID: 32034845 PMCID: PMC7415788 DOI: 10.1111/pbi.13357] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 01/07/2020] [Accepted: 01/19/2020] [Indexed: 05/18/2023]
Abstract
Grain/seed yield and plant stress tolerance are two major traits that determine the yield potential of many crops. In cereals, grain size is one of the key factors affecting grain yield. Here, we identify and characterize a newly discovered gene Rice Big Grain 1 (RBG1) that regulates grain and organ development, as well as abiotic stress tolerance. Ectopic expression of RBG1 leads to significant increases in the size of not only grains but also other major organs such as roots, shoots and panicles. Increased grain size is primarily due to elevated cell numbers rather than cell enlargement. RBG1 is preferentially expressed in meristematic and proliferating tissues. Ectopic expression of RBG1 promotes cell division, and RBG1 co-localizes with microtubules known to be involved in cell division, which may account for the increase in organ size. Ectopic expression of RBG1 also increases auxin accumulation and sensitivity, which facilitates root development, particularly crown roots. Moreover, overexpression of RBG1 up-regulated a large number of heat-shock proteins, leading to enhanced tolerance to heat, osmotic and salt stresses, as well as rapid recovery from water-deficit stress. Ectopic expression of RBG1 regulated by a specific constitutive promoter, GOS2, enhanced harvest index and grain yield in rice. Taken together, we have discovered that RBG1 regulates two distinct and important traits in rice, namely grain yield and stress tolerance, via its effects on cell division, auxin and stress protein induction.
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Affiliation(s)
- Shuen‐Fang Lo
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Ming‐Lung Cheng
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Department of Life SciencesNational Cheng Kung UniversityTainanTaiwan, ROC
| | | | - Yi‐Shih Chen
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Kuo‐Wei Lee
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Ya‐Fang Hong
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Yu Hsiao
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - An‐Shan Hsiao
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Pei‐Jing Chen
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Lai‐In Wong
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Nan‐Chen Chen
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | | | - Tuan‐Hua David Ho
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
- Department of Life SciencesNational Cheng Kung UniversityTainanTaiwan, ROC
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Department of Life SciencesNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Su‐May Yu
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
- Department of Life SciencesNational Cheng Kung UniversityTainanTaiwan, ROC
- Department of Life SciencesNational Chung Hsing UniversityTaichungTaiwan, ROC
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11
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Amartuvshin O, Lin C, Hsu S, Kao S, Chen A, Tang W, Chou H, Chang D, Hsu Y, Hsiao B, Rastegari E, Lin K, Wang Y, Yao C, Chen G, Chen B, Hsu H. Aging shifts mitochondrial dynamics toward fission to promote germline stem cell loss. Aging Cell 2020; 19:e13191. [PMID: 32666649 PMCID: PMC7431834 DOI: 10.1111/acel.13191] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/20/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Changes in mitochondrial dynamics (fusion and fission) are known to occur during stem cell differentiation; however, the role of this phenomenon in tissue aging remains unclear. Here, we report that mitochondrial dynamics are shifted toward fission during aging of Drosophila ovarian germline stem cells (GSCs), and this shift contributes to aging-related GSC loss. We found that as GSCs age, mitochondrial fragmentation and expression of the mitochondrial fission regulator, Dynamin-related protein (Drp1), are both increased, while mitochondrial membrane potential is reduced. Moreover, preventing mitochondrial fusion in GSCs results in highly fragmented depolarized mitochondria, decreased BMP stemness signaling, impaired fatty acid metabolism, and GSC loss. Conversely, forcing mitochondrial elongation promotes GSC attachment to the niche. Importantly, maintenance of aging GSCs can be enhanced by suppressing Drp1 expression to prevent mitochondrial fission or treating with rapamycin, which is known to promote autophagy via TOR inhibition. Overall, our results show that mitochondrial dynamics are altered during physiological aging, affecting stem cell homeostasis via coordinated changes in stemness signaling, niche contact, and cellular metabolism. Such effects may also be highly relevant to other stem cell types and aging-induced tissue degeneration.
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Affiliation(s)
- Oyundari Amartuvshin
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan
- Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
| | - Chi‐Hung Lin
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
| | - Shao‐Chun Hsu
- Imaging Core Facility at the Institute of Cellular and Organismic BiologyAcademia SinicaTaipeiTaiwan
| | - Shih‐Han Kao
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
- Present address:
Institute of ChemistryAcademia SinicaTaipeiTaiwan
| | - Alvin Chen
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
| | - Wei‐Chun Tang
- Research Center for Applied ScienceAcademia SinicaTaipeiTaiwan
| | - Han‐Lin Chou
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
| | - Dong‐Lin Chang
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
- The Affiliated Senior High School of National Taiwan Normal UniversityTaipeiTaiwan
| | - Yen‐Yang Hsu
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
- The Affiliated Senior High School of National Taiwan Normal UniversityTaipeiTaiwan
| | - Bai‐Shiou Hsiao
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
- The Affiliated Senior High School of National Taiwan Normal UniversityTaipeiTaiwan
| | | | - Kun‐Yang Lin
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
| | - Yu‐Ting Wang
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan
- Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
| | - Chi‐Kuang Yao
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
| | - Guang‐Chao Chen
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
| | - Bi‐Chang Chen
- Research Center for Applied ScienceAcademia SinicaTaipeiTaiwan
| | - Hwei‐Jan Hsu
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan
- Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
- Institute of Cellular and Organismic BiologyTaipeiTaiwan
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12
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Sharma R, Yeh K. The dual benefit of a dominant mutation in Arabidopsis IRON DEFICIENCY TOLERANT1 for iron biofortification and heavy metal phytoremediation. Plant Biotechnol J 2020; 18:1200-1210. [PMID: 31671241 PMCID: PMC7152604 DOI: 10.1111/pbi.13285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 05/12/2023]
Abstract
One of the goals of biofortification is to generate iron-enriched crops to combat growth and developmental defects especially iron (Fe) deficiency anaemia. Fe-fortification of food is challenging because soluble Fe is unstable and insoluble Fe is nonbioavailable. Genetic engineering is an alternative approach for Fe-biofortification, but so far strategies to increase Fe content have only encompassed a few genes with limited success. In this study, we demonstrate that the ethyl methanesulfonate (EMS) mutant, iron deficiency tolerant1 (idt1), can accumulate 4-7 times higher amounts of Fe than the wild type in roots, shoots and seeds, and exhibits the metal tolerance and iron accumulation (Metina) phenotype in Arabidopsis. Fe-regulated protein stability and nuclear localisation of the upstream transcriptional regulator bHLH34 were uncovered. The C to T transition mutation resulting in substitution of alanine to valine at amino acid position 320 of bHLH34 (designated as IDT1A320V ) in a conserved motif among mono- and dicots was found to be responsible for a dominant phenotype that possesses constitutive activation of the Fe regulatory pathway. Overexpression of IDT1A320V in Arabidopsis and tobacco led to the Metina phenotype; a phenotype that has escalated specificity towards optimising Fe homeostasis and may be useful in Fe-biofortification. Knowledge of the high tolerance and accumulation of heavy metals of this mutant can aid the development of tools for phytoremediation of contaminants.
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Affiliation(s)
- Reena Sharma
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
- Molecular and Biological Agricultural Sciences ProgramTaiwan International Graduate ProgramAcademia Sinica and National Chung Hsing UniversityTaipeiTaiwan
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
| | - Kuo‐Chen Yeh
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
- Molecular and Biological Agricultural Sciences ProgramTaiwan International Graduate ProgramAcademia Sinica and National Chung Hsing UniversityTaipeiTaiwan
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
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13
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Chan M, Huang W, Wang J, Liu R, Hsiao M. Next-Generation Cancer-Specific Hybrid Theranostic Nanomaterials: MAGE-A3 NIR Persistent Luminescence Nanoparticles Conjugated to Afatinib for In Situ Suppression of Lung Adenocarcinoma Growth and Metastasis. Adv Sci (Weinh) 2020; 7:1903741. [PMID: 32382487 PMCID: PMC7201263 DOI: 10.1002/advs.201903741] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 05/19/2023]
Abstract
The rate of lung cancer has gradually increased in recent years, with an average annual increase of 15%. Afatinib (AFT) plays a key role in preventing non-small cell lung carcinoma (NSCLC) growth and spread. To increase the efficiency of drug loading and NSCLC cell tracking, near infrared-persistent luminescence nanomaterials (NIR PLNs), a silica shell-assisted synthetic route for mono-dispersal, are developed and used in the nanovehicle. After optimizing their physical and chemical properties, the NIR PLNs are able to absorb light energy and emit NIR luminescence for several hours. In this research, NIR PLNs are functionalized for drug-carrying capabilities. Effective accumulation of target drugs, such as AFT, using PLN nanomaterials can lead to unique anticancer therapeutic benefits (AFT-PLN). To minimize side effects and increase drug accumulation, nanomaterials with targeting abilities are used instead of simple drugs to inhibit the growth of tumor cells. Thus, the specific targeting aptamer, MAGE-A3 (MAp) is identified, and the PLN to increase its targeting ability (AFT-PLN@MAp) accordingly modified. The advancement of nanoscale techniques in the field of lung cancer is urgently needed; this research presents a plausible diagnostic strategy and a novel method for therapeutic administration.
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Affiliation(s)
| | - Wen‐Tse Huang
- Department of ChemistryNational Taiwan UniversityTaipei106Taiwan
| | - Jing Wang
- Ministry of Education Key Laboratory of Bioinorganic and Synthetic ChemistryState Key Laboratory of Optoelectronic Materials and TechnologiesSchool of ChemistrySun Yat‐Sen UniversityGuangzhouGuangdong510275China
| | - Ru‐Shi Liu
- Department of ChemistryNational Taiwan UniversityTaipei106Taiwan
- Department of Mechanical EngineeringGraduate Institute of Manufacturing TechnologyNational Taipei University of TechnologyTaipei106Taiwan
| | - Michael Hsiao
- Genomics Research CenterAcademia SinicaTaipei115Taiwan
- Department of BiochemistryCollege of MedicineKaohsiung Medical UniversityKaohsiung807Taiwan
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14
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Campos‐Soriano L, Bundó M, Bach‐Pages M, Chiang S, Chiou T, San Segundo B. Phosphate excess increases susceptibility to pathogen infection in rice. Mol Plant Pathol 2020; 21:555-570. [PMID: 32072745 PMCID: PMC7060143 DOI: 10.1111/mpp.12916] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/18/2019] [Accepted: 01/10/2020] [Indexed: 05/08/2023]
Abstract
Phosphorus (P) is an essential nutrient for plant growth and productivity. Due to soil fixation, however, phosphorus availability in soil is rarely sufficient to sustain high crop yields. The overuse of fertilizers to circumvent the limited bioavailability of phosphate (Pi) has led to a scenario of excessive soil P in agricultural soils. Whereas adaptive responses to Pi deficiency have been deeply studied, less is known about how plants adapt to Pi excess and how Pi excess might affect disease resistance. We show that high Pi fertilization, and subsequent Pi accumulation, enhances susceptibility to infection by the fungal pathogen Magnaporthe oryzae in rice. This fungus is the causal agent of the blast disease, one of the most damaging diseases of cultivated rice worldwide. Equally, MIR399f overexpression causes an increase in Pi content in rice leaves, which results in enhanced susceptibility to M. oryzae. During pathogen infection, a weaker activation of defence-related genes occurs in rice plants over-accumulating Pi in leaves, which is in agreement with the phenotype of blast susceptibility observed in these plants. These data support that Pi, when in excess, compromises defence mechanisms in rice while demonstrating that miR399 functions as a negative regulator of rice immunity. The two signalling pathways, Pi signalling and defence signalling, must operate in a coordinated manner in controlling disease resistance. This information provides a basis to understand the molecular mechanisms involved in immunity in rice plants under high Pi fertilization, an aspect that should be considered in management of the rice blast disease.
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Affiliation(s)
- Lidia Campos‐Soriano
- Centre for Research in Agricultural GenomicsCSIC‐IRTA‐UAB‐UBUniversitat Autònoma de BarcelonaBellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Mireia Bundó
- Centre for Research in Agricultural GenomicsCSIC‐IRTA‐UAB‐UBUniversitat Autònoma de BarcelonaBellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Marcel Bach‐Pages
- Centre for Research in Agricultural GenomicsCSIC‐IRTA‐UAB‐UBUniversitat Autònoma de BarcelonaBellaterra (Cerdanyola del Vallés)BarcelonaSpain
- Present address:
Department of Plant SciencesUniversity of OxfordOxfordUK
| | - Su‐Fen Chiang
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
| | - Tzyy‐Jen Chiou
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
| | - Blanca San Segundo
- Centre for Research in Agricultural GenomicsCSIC‐IRTA‐UAB‐UBUniversitat Autònoma de BarcelonaBellaterra (Cerdanyola del Vallés)BarcelonaSpain
- Consejo Superior de Investigaciones CientíficasBarcelonaSpain
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15
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Pai H, Jean W, Lee Y, Chang YA, Lin N. Genome-wide analysis of small RNAs from Odontoglossum ringspot virus and Cymbidium mosaic virus synergistically infecting Phalaenopsis. Mol Plant Pathol 2020; 21:188-205. [PMID: 31724809 PMCID: PMC6988431 DOI: 10.1111/mpp.12888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) are the two most prevalent viruses infecting orchids and causing economic losses worldwide. Mixed infection of CymMV and ORSV could induce intensified symptoms as early at 10 days post-inoculation in inoculated Phalaenopsis amabilis, where CymMV pathogenesis was unilaterally enhanced by ORSV. To reveal the antiviral RNA silencing activity in orchids, we characterized the viral small-interfering RNAs (vsiRNAs) from CymMV and ORSV singly or synergistically infecting P. amabilis. We also temporally classified the inoculated leaf-tip tissues and noninoculated adjacent tissues as late and early stages of infection, respectively. Regardless of early or late stage with single or double infection, CymMV and ORSV vsiRNAs were predominant in 21- and 22-nt sizes, with excess positive polarity and under-represented 5'-guanine. While CymMV vsiRNAs mainly derived from RNA-dependent RNA polymerase-coding regions, ORSV vsiRNAs encompassed the coat protein gene and 3'-untranslated region, with a specific hotspot residing in the 3'-terminal pseudoknot. With double infection, CymMV vsiRNAs increased more than 5-fold in number with increasing virus titres. Most vsiRNA features remained unchanged with double inoculation, but additional ORSV vsiRNA hotspot peaks were prominent. The potential vsiRNA-mediated regulation of the novel targets in double-infected tissues thereby provides a different view of CymMV and ORSV synergism. Hence, temporally profiled vsiRNAs from taxonomically distinct CymMV and ORSV illustrate active antiviral RNA silencing in their natural host, Phalaenopsis, during both early and late stages of infection. Our findings provide insights into offence-defence interactions among CymMV, ORSV and orchids.
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Affiliation(s)
- Hsuan Pai
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan11529
| | - Wen‐Han Jean
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan11529
| | - Yun‐Shien Lee
- Department of BiotechnologyMing Chuan UniversityTao‐YuanTaiwan33348
| | - Yao‐Chien Alex Chang
- Department of Horticulture and Landscape ArchitectureNational Taiwan UniversityTaipeiTaiwan10617
| | - Na‐Sheng Lin
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan11529
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16
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He R, Lai X, Sun C, Kung T, Hong J, Jheng Y, Liao W, Chen J, Liao Y, Tu P, Huang JJ. Nanoscopic Insights of Amphiphilic Peptide against the Oligomer Assembly Process to Treat Huntington's Disease. Adv Sci (Weinh) 2020; 7:1901165. [PMID: 31993280 PMCID: PMC6974936 DOI: 10.1002/advs.201901165] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/07/2019] [Indexed: 05/12/2023]
Abstract
Finding an effective therapeutic regimen is an urgent demand for various neurodegenerative disorders including Huntington's disease (HD). For the difficulties in observing the dynamic aggregation and oligomerization process of mutant Huntingtin (mHtt) in vivo, the evaluation of potential drugs at the molecular protein level is usually restricted. By combing lifetime-based fluorescence microscopies and biophysical tools, it is showcased that a designed amphiphilic peptide, which targets the mHtt at an early stage, can perturb the oligomer assembly process nanoscopically, suppress the amyloid property of mHtt, conformationally transform the oligomers and/or aggregates of mHtt, and ameliorate mHtt-induced neurological damage and aggregation in cell and HD mouse models. It is also found that this amphiphilic peptide is able to transport to the brain and rescue the memory deficit through intranasal administration, indicating its targeting specificity in vivo. In summary, a biophotonic platform is provided to investigate the oligomerization/aggregation process in detail that offers insight into the design and effect of a targeted therapeutic agent for Huntington's disease.
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Affiliation(s)
- Ruei‐Yu He
- Institute of ChemistryAcademia SinicaTaipei11529Taiwan
| | - Xiang‐Me Lai
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
- Division of UrologyDepartment of SurgeryTri‐Service General HospitalNational Defense Medical CenterTaipei11490Taiwan
| | - Chia‐Sui Sun
- Institute of ChemistryAcademia SinicaTaipei11529Taiwan
| | - Te‐Shien Kung
- Institute of ChemistryAcademia SinicaTaipei11529Taiwan
- Department of Chemical EngineeringNational Taiwan University of Science and TechnologyTaipei10607Taiwan
| | - Jhu‐Ying Hong
- Institute of ChemistryAcademia SinicaTaipei11529Taiwan
| | - Yu‐Song Jheng
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
| | - Wei‐Neng Liao
- Institute of Biomedical Engineering and NanomedicineNational Health Research InstitutesMiaoli35053Taiwan
| | - Jen‐Kun Chen
- Division of UrologyDepartment of SurgeryTri‐Service General HospitalNational Defense Medical CenterTaipei11490Taiwan
- Institute of Biomedical Engineering and NanomedicineNational Health Research InstitutesMiaoli35053Taiwan
| | - Yung‐Feng Liao
- Institute of Cellular and Organismic BiologyAcademia SinicaTaipei11529Taiwan
| | - Pang‐Hsien Tu
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
- Division of UrologyDepartment of SurgeryTri‐Service General HospitalNational Defense Medical CenterTaipei11490Taiwan
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17
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Dang V, Cohanim AB, Fontana S, Privman E, Wang J. Has gene expression neofunctionalization in the fire ant antennae contributed to queen discrimination behavior? Ecol Evol 2019; 9:12754-12766. [PMID: 31788211 PMCID: PMC6875580 DOI: 10.1002/ece3.5748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/18/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022] Open
Abstract
Queen discrimination behavior in the fire ant Solenopsis invicta maintains its two types of societies: colonies with one (monogyne) or many (polygyne) queens, yet the underlying genetic mechanism is poorly understood. This behavior is controlled by two supergene alleles, SB and Sb, with ~600 genes. Polygyne workers, having either the SB/SB or SB/Sb genotype, accept additional SB/Sb queens into their colonies but kill SB/SB queens. In contrast, monogyne workers, all SB/SB, reject all additional queens regardless of genotype. Because the SB and Sb alleles have suppressed recombination, determining which genes within the supergene mediate this differential worker behavior is difficult. We hypothesized that the alternate worker genotypes sense queens differently because of the evolution of differential expression of key genes in their main sensory organ, the antennae. To identify such genes, we sequenced RNA from four replicates of pooled antennae from three classes of workers: monogyne SB/SB, polygyne SB/SB, and polygyne SB/Sb. We identified 81 differentially expressed protein-coding genes with 13 encoding potential chemical metabolism or perception proteins. We focused on the two odorant perception genes: an odorant receptor SiOR463 and an odorant-binding protein SiOBP12. We found that SiOR463 has been lost in the Sb genome. In contrast, SiOBP12 has an Sb-specific duplication, SiOBP12b', which is expressed in the SB/Sb worker antennae, while both paralogs are expressed in the body. Comparisons with another fire ant species revealed that SiOBP12b' antennal expression is specific to S. invicta and suggests that queen discrimination may have evolved, in part, through expression neofunctionalization.
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Affiliation(s)
- Viet‐Dai Dang
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Biodiversity Taiwan International Graduate Program, Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
- Department of ZoologySouthern Institute of EcologyVietnam Academy of Science and TechnologyHochiminhVietnam
| | - Amir B. Cohanim
- Department of Evolutionary and Environmental BiologyInstitute of EvolutionUniversity of HaifaHaifaIsrael
| | - Silvia Fontana
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Biodiversity Taiwan International Graduate Program, Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Eyal Privman
- Department of Evolutionary and Environmental BiologyInstitute of EvolutionUniversity of HaifaHaifaIsrael
| | - John Wang
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
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18
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Abstract
Human RNA exoribonuclease 2 (Rexo2) is an evolutionarily conserved 3'-to-5' DEDDh-family exonuclease located primarily in mitochondria. Rexo2 degrades small RNA oligonucleotides of <5 nucleotides (nanoRNA) in a way similar to Escherichia coli Oligoribonuclease (ORN), suggesting that it plays a role in RNA turnover in mitochondria. However, how Rexo2 preferentially binds and degrades nanoRNA remains elusive. Here, we show that Rexo2 binds small RNA and DNA oligonucleotides with the highest affinity, and it is most robust in degrading small nanoRNA into mononucleotides in the presence of magnesium ions. We further determined three crystal structures of Rexo2 in complex with single-stranded RNA or DNA at resolutions of 1.8-2.2 Å. Rexo2 forms a homodimer and interacts mainly with the last two 3'-end nucleobases of substrates by hydrophobic and π-π stacking interactions via Leu53, Trp96, and Tyr164, signifying its preference in binding and degrading short oligonucleotides without sequence specificity. Crystal structure of Rexo2 is highly similar to that of the RNA-degrading enzyme ORN, revealing a two-magnesium-ion-dependent hydrolysis mechanism. This study thus provides the molecular basis for human Rexo2, showing how it binds and degrades nanoRNA into nucleoside monophosphates and plays a crucial role in RNA salvage pathways in mammalian mitochondria.
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MESH Headings
- 14-3-3 Proteins/chemistry
- 14-3-3 Proteins/genetics
- 14-3-3 Proteins/metabolism
- Binding Sites
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cations, Divalent
- Cloning, Molecular
- Crystallography, X-Ray
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Exoribonucleases/chemistry
- Exoribonucleases/genetics
- Exoribonucleases/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Humans
- Hydrolysis
- Hydrophobic and Hydrophilic Interactions
- Magnesium/chemistry
- Magnesium/metabolism
- Mitochondria/chemistry
- Mitochondria/metabolism
- Mitochondrial Proteins/chemistry
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Models, Molecular
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/genetics
- Oligoribonucleotides/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Multimerization
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
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Affiliation(s)
- Lee-Ya Chu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin Chu, Taiwan 30013, Republic of China
| | - Sashank Agrawal
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 11490, Republic of China
| | - Yi-Ping Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
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19
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Li CL, Yang WZ, Shi Z, Yuan HS. Tudor staphylococcal nuclease is a structure-specific ribonuclease that degrades RNA at unstructured regions during microRNA decay. RNA 2018; 24:739-748. [PMID: 29440319 PMCID: PMC5900569 DOI: 10.1261/rna.064501.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Tudor staphylococcal nuclease (TSN) is an evolutionarily conserved ribonuclease in eukaryotes that is composed of five staphylococcal nuclease-like domains (SN1-SN5) and a Tudor domain. TSN degrades hyper-edited double-stranded RNA, including primary miRNA precursors containing multiple I•U and U•I pairs, and mature miRNA during miRNA decay. However, how TSN binds and degrades its RNA substrates remains unclear. Here, we show that the C. elegans TSN (cTSN) is a monomeric Ca2+-dependent ribonuclease, cleaving RNA chains at the 5'-side of the phosphodiester linkage to produce degraded fragments with 5'-hydroxyl and 3'-phosphate ends. cTSN degrades single-stranded RNA and double-stranded RNA containing mismatched base pairs, but is not restricted to those containing multiple I•U and U•I pairs. cTSN has at least two catalytic active sites located in the SN1 and SN3 domains, since mutations of the putative Ca2+-binding residues in these two domains strongly impaired its ribonuclease activity. We further show by small-angle X-ray scattering that rice osTSN has a flexible two-lobed structure with open to closed conformations, indicating that TSN may change its conformation upon RNA binding. We conclude that TSN is a structure-specific ribonuclease targeting not only single-stranded RNA, but also unstructured regions of double-stranded RNA. This study provides the molecular basis for how TSN cooperates with RNA editing to eliminate duplex RNA in cell defense, and how TSN selects and degrades RNA during microRNA decay.
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Affiliation(s)
- Chia-Lung Li
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Zhonghao Shi
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, ROC
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