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Cui S, Song P, Wang C, Chen S, Hao B, Xu Z, Cai L, Chen X, Zhu S, Gan X, Dong H, Hu Y, Zhou L, Hou H, Tian Y, Liu X, Chen L, Liu S, Jiang L, Wang H, Jia G, Zhou S, Wan J. The RNA binding protein EHD6 recruits the m 6A reader YTH07 and sequesters OsCOL4 mRNA into phase-separated ribonucleoprotein condensates to promote rice flowering. MOLECULAR PLANT 2024; 17:935-954. [PMID: 38720462 DOI: 10.1016/j.molp.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 03/31/2024] [Accepted: 05/05/2024] [Indexed: 05/31/2024]
Abstract
N6-Methyladenosine (m6A) is one of the most abundant modifications of eukaryotic mRNA, but its comprehensive biological functionality remains further exploration. In this study, we identified and characterized a new flowering-promoting gene, EARLY HEADING DATE6 (EHD6), in rice. EHD6 encodes an RNA recognition motif (RRM)-containing RNA binding protein that is localized in the non-membranous cytoplasm ribonucleoprotein (RNP) granules and can bind both m6A-modified RNA and unmodified RNA indiscriminately. We found that EHD6 can physically interact with YTH07, a YTH (YT521-B homology) domain-containing m6A reader. We showed that their interaction enhances the binding of an m6A-modified RNA and triggers relocation of a portion of YTH07 from the cytoplasm into RNP granules through phase-separated condensation. Within these condensates, the mRNA of a rice flowering repressor, CONSTANS-like 4 (OsCOL4), becomes sequestered, leading to a reduction in its protein abundance and thus accelerated flowering through the Early heading date 1 pathway. Taken together, these results not only shed new light on the molecular mechanism of efficient m6A recognition by the collaboration between an RNA binding protein and YTH family m6A reader, but also uncover the potential for m6A-mediated translation regulation through phase-separated ribonucleoprotein condensation in rice.
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Affiliation(s)
- Song Cui
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory for Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Center of RNA Biology, Peking University, Beijing, China
| | - Chaolong Wang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Saihua Chen
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Benyuan Hao
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhuang Xu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Cai
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Xu Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Center of RNA Biology, Peking University, Beijing, China
| | - Shanshan Zhu
- State Key Laboratory for Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiangchao Gan
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China; Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Hui Dong
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan Hu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Zhou
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Haigang Hou
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Liangming Chen
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyang Wang
- State Key Laboratory for Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Center of RNA Biology, Peking University, Beijing, China.
| | - Shirong Zhou
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory for Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Xu L, Xiong X, Liu T, Cao J, Yu Y. Heterologous Expression of Two Brassica campestris CCCH Zinc-Finger Proteins in Arabidopsis Induces Cytoplasmic Foci and Causes Pollen Abortion. Int J Mol Sci 2023; 24:16862. [PMID: 38069184 PMCID: PMC10706035 DOI: 10.3390/ijms242316862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
The membrane-less organelles in cytoplasm that are presented as cytoplasmic foci were successively identified. Although multiple CCCH zinc-finger proteins have been found to be localized in cytoplasmic foci, the relationship between their specific localization and functions still needs further clarification. Here, we report that the heterologous expression of two Brassica campestris CCCH zinc-finger protein genes (BcMF30a and BcMF30c) in Arabidopsis thaliana can affect microgametogenesis by involving the formation of cytoplasmic foci. By monitoring the distribution of proteins and observing pollen phenotypes, we found that, when these two proteins were moderately expressed in pollen, they were mainly dispersed in the cytoplasm, and the pollen developed normally. However, high expression induced the assembly of cytoplasmic foci, leading to pollen abortion. These findings suggested that the continuous formation of BcMF30a/BcMF30c-associated cytoplasmic foci due to high expression was the inducement of male sterility. A co-localization analysis further showed that these two proteins can be recruited into two well-studied cytoplasmic foci, processing bodies (PBs), and stress granules (SGs), which were confirmed to function in mRNA metabolism. Together, our data suggested that BcMF30a and BcMF30c play component roles in the assembly of pollen cytoplasmic foci. Combined with our previous study on the homologous gene of BcMF30a/c in Arabidopsis, we concluded that the function of these homologous genes is conserved and that cytoplasmic foci containing BcMF30a/c may participate in the regulation of gene expression in pollen by regulating mRNA metabolism.
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Affiliation(s)
- Liai Xu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China;
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (X.X.); (T.L.)
| | - Xingpeng Xiong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (X.X.); (T.L.)
| | - Tingting Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (X.X.); (T.L.)
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (X.X.); (T.L.)
| | - Youjian Yu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China;
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3
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Jiang L, Cai H, Zhou W, Li Z, Zhang L, Bi H. RNA-Targeting Carbon Dots for Live-Cell Imaging of Granule Dynamics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210776. [PMID: 36645339 DOI: 10.1002/adma.202210776] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/02/2023] [Indexed: 05/26/2023]
Abstract
It is significant to monitor the different RNA granules dynamics and phase separation process inside cells under various stresses, for example, oxidative stress. The current small-molecule RNA probes work well only in fixed cells and usually encounter problems such as insufficient stability and biocompatibility, and thus a specific RNA-targeting fluorescent nanoprobe that can be used in the living cells is urgently desired. Here, the de novo design and microwave-assisted synthesis of a novel RNA-targeting, red-emissive carbon dots (named as M-CDs) are reported by choosing neutral red and levofloxacin as precursors. The as-synthesized M-CDs is water-soluble with a high fluorescence quantum yield of 22.83% and can selectively bind to RNA resulting in an enhanced red fluorescence. More interestingly, such an RNA-targeting, red-emissive M-CDs can be fast internalized into cells within 5 s and thus used for real-time imaging the dynamic process of intracellular stress granules under oxidative stress, revealing some characteristics of granules that have not been identified by previously reported RNA and protein biomarkers. This research paves a new pathway for visualizing bulk RNA dynamics and studying phase-separation behaviors in living cells by rational design of the fluorescent carbon dots in terms of structure and functionality.
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Affiliation(s)
- Lei Jiang
- School of Chemistry and Chemical Engineering, Anhui University, 111 Jiulong Road, Hefei, 230601, P. R. China
| | - Hao Cai
- School of Materials Science and Engineering, Anhui University, 111 Jiulong Road, Hefei, 23060, P. R. China
| | - Wanwan Zhou
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Huangshan Road, Hefei, Anhui, 230027, P. R. China
| | - Zijian Li
- School of Materials Science and Engineering, Anhui University, 111 Jiulong Road, Hefei, 23060, P. R. China
| | - Liang Zhang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Huangshan Road, Hefei, Anhui, 230027, P. R. China
| | - Hong Bi
- School of Materials Science and Engineering, Anhui University, 111 Jiulong Road, Hefei, 23060, P. R. China
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Asano-Inami E, Yokoi A, Sugiyama M, Hyodo T, Hamaguchi T, Kajiyama H. The association of UBAP2L and G3BP1 mediated by small nucleolar RNA is essential for stress granule formation. Commun Biol 2023; 6:415. [PMID: 37059803 PMCID: PMC10104854 DOI: 10.1038/s42003-023-04754-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 03/24/2023] [Indexed: 04/16/2023] Open
Abstract
Stress granules (SGs) are dynamic, non-membranous structures composed of non-translating mRNAs and various proteins and play critical roles in cell survival under stressed conditions. Extensive proteomics analyses have been performed to identify proteins in SGs; however, the molecular functions of these components in SG formation remain unclear. In this report, we show that ubiquitin-associated protein 2-like (UBAP2L) is a crucial component of SGs. UBAP2L localized to SGs in response to various stresses, and its depletion significantly suppressed SG organization. Proteomics and RNA sequencing analyses found that UBAP2L formed a protein-RNA complex with Ras-GTP-activating protein SH3 domain binding protein 1 (G3BP1) and small nucleolar RNAs (snoRNAs). In vitro binding analysis demonstrated that snoRNAs were required for UBAP2L association with G3BP1. In addition, decreased expression of snoRNAs reduced the interaction between UBAP2L and G3BP1 and suppressed SG formation. Our results reveal a critical role of SG component, the UBAP2L/snoRNA/G3BP1 protein-RNA complex, and provide new insights into the regulation of SG assembly.
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Affiliation(s)
- Eri Asano-Inami
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
- Bell Research Center for Reproductive Health and Cancer, Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
| | - Akira Yokoi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
- Institute for Advanced Research, Nagoya University, Nagoya, Japan.
| | - Mai Sugiyama
- Bell Research Center for Reproductive Health and Cancer, Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
| | - Toshinori Hyodo
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Aichi, 480-1195, Japan
| | - Tomonari Hamaguchi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
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Xu W, Jian S, Li J, Wang Y, Zhang M, Xia K. Genomic Identification of CCCH-Type Zinc Finger Protein Genes Reveals the Role of HuTZF3 in Tolerance of Heat and Salt Stress of Pitaya (Hylocereus polyrhizus). Int J Mol Sci 2023; 24:ijms24076359. [PMID: 37047333 PMCID: PMC10094633 DOI: 10.3390/ijms24076359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Pitaya (Hylocereus polyrhizus) is cultivated in a broad ecological range, due to its tolerance to drought, heat, and poor soil. The zinc finger proteins regulate gene expression at the transcriptional and post-transcriptional levels, by interacting with DNA, RNA, and proteins, to play roles in plant growth and development, and stress response. Here, a total of 81 CCCH-type zinc finger protein genes were identified from the pitaya genome. Transcriptomic analysis showed that nine of them, including HuTZF3, responded to both salt and heat stress. RT-qPCR results showed that HuTZF3 is expressed in all tested organs of pitaya, with a high level in the roots and stems, and confirmed that expression of HuTZF3 is induced by salt and heat stress. Subcellular localization showed that HuTZF3 is targeted in the processing bodies (PBs) and stress granules (SGs). Heterologous expression of HuTZF3 could improve both salt and heat tolerance in Arabidopsis, reduce oxidative stress, and improve the activity of catalase and peroxidase. Therefore, HuTZF3 may be involved in post-transcriptional regulation via localizing to PBs and SGs, contributing to both salt and heat tolerance in pitaya.
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Affiliation(s)
- Weijuan Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuguang Jian
- South China National Botanical Garden, Guangzhou 510650, China
- CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jianyi Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yusang Wang
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- Correspondence: (M.Z.); (K.X.); Tel./Fax: +86-20-37252891 (M.Z.)
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- Correspondence: (M.Z.); (K.X.); Tel./Fax: +86-20-37252891 (M.Z.)
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Wang L, Guzmán M, Sola I, Enjuanes L, Zuñiga S. Cytoplasmic ribonucleoprotein complexes, RNA helicases and coronavirus infection. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.1078454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA metabolism in the eukaryotic cell includes the formation of ribonucleoprotein complexes (RNPs) that, depending on their protein components, have a different function. Cytoplasmic RNPs, such as stress granules (SGs) or P-bodies (PBs) are quite relevant during infections modulating viral and cellular RNA expression and as key players in the host cell antiviral response. RNA helicases are abundant components of RNPs and could have a significant effect on viral infection. This review focuses in the role that RNPs and RNA helicases have during coronavirus (CoVs) infection. CoVs are emerging highly pathogenic viruses with a large single-stranded RNA genome. During CoV infection, a complex network of RNA-protein interactions in different RNP structures is established. In general, RNA helicases and RNPs have an antiviral function, but there is limited knowledge on whether the viral protein interactions with cell components are mediators of this antiviral effect or are part of the CoV antiviral counteraction mechanism. Additional data is needed to elucidate the role of these RNA-protein interactions during CoV infection and their potential contribution to viral replication or pathogenesis.
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Xu L, Liu T, Xiong X, Shen X, Huang L, Yu Y, Cao J. Highly Overexpressed AtC3H18 Impairs Microgametogenesis via Promoting the Continuous Assembly of mRNP Granules. FRONTIERS IN PLANT SCIENCE 2022; 13:932793. [PMID: 35909782 PMCID: PMC9335048 DOI: 10.3389/fpls.2022.932793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Plant CCCH zinc-finger proteins form a large family of regulatory proteins function in many aspects of plant growth, development and environmental responses. Despite increasing reports indicate that many CCCH zinc-finger proteins exhibit similar subcellular localization of being localized in cytoplasmic foci, the underlying molecular mechanism and the connection between this specific localization pattern and protein functions remain largely elusive. Here, we identified another cytoplasmic foci-localized CCCH zinc-finger protein, AtC3H18, in Arabidopsis thaliana. AtC3H18 is predominantly expressed in developing pollen during microgametogenesis. Although atc3h18 mutants did not show any abnormal phenotype, possibly due to redundant gene(s), aberrant AtC3H18 expression levels caused by overexpression resulted in the assembly of AtC3H18-positive granules in a dose-dependent manner, which in turn led to male sterility phenotype, highlighting the importance of fine-tuned AtC3H18 expression. Further analyzes demonstrated that AtC3H18-positive granules are messenger ribonucleoprotein (mRNP) granules, since they can exhibit liquid-like physical properties, and are associated with another two mRNP granules known as processing bodies (PBs) and stress granules (SGs), reservoirs of translationally inhibited mRNAs. Moreover, the assembly of AtC3H18-positive granules depends on mRNA availability. Combined with our previous findings on the AtC3H18 homologous genes in Brassica campestris, we concluded that appropriate expression level of AtC3H18 during microgametogenesis is essential for normal pollen development, and we also speculated that AtC3H18 may act as a key component of mRNP granules to modulate pollen mRNAs by regulating the assembly/disassembly of mRNP granules, thereby affecting pollen development.
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Affiliation(s)
- Liai Xu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Tingting Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Xingpeng Xiong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Xiuping Shen
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Youjian Yu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
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Schwed-Gross A, Hamiel H, Faber GP, Angel M, Ben-Yishay R, Benichou JIC, Ishay-Ronen D, Shav-Tal Y. Glucocorticoids enhance chemotherapy-driven stress granule assembly and impair granule dynamics leading to cell death. J Cell Sci 2022; 135:276097. [PMID: 35713120 PMCID: PMC9450892 DOI: 10.1242/jcs.259629] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/13/2022] [Indexed: 11/20/2022] Open
Abstract
Stress granules (SGs) can assemble in cancer cells upon chemotoxic stress. Glucocorticoids function during stress responses and are administered with chemotherapies. The roles of glucocorticoids in SG assembly and disassembly pathways are unknown. We examined whether combining glucocorticoids such as cortisone with chemotherapies from the vinca alkaloid family, which dismantle the microtubule network, affects SG assembly and disassembly pathways and influences cell viability in cancer cells and human-derived organoids. Cortisone augmented SG formation when combined with vinorelbine (VRB). Live-cell imaging showed that cortisone increased SG assembly rates but reduced SG clearance rates after stress, by increasing protein residence times within the SGs. Mechanistically, VRB and cortisone signaled through the integrated stress response mediated by eIF2α (also known as EIF2S1), yet induced different kinases, with cortisone activating the GCN2 kinase (also known as EIF2AK4). Cortisone increased VRB-induced cell death and reduced the population of cells trapped in mitotic catastrophe. These effects were mediated by the core SG proteins G3BP1 and G3BP2. In conclusion, glucocorticoids induce SG assembly and cell death when administered with chemotherapies, suggesting that combining glucocorticoids with chemotherapies can enhance cancer cell chemosensitivity. Summary: Combining cortisone with the chemotherapy vinorelbine enhances the assembly of stress granules that are less likely to be cleared from the cells, augmenting vinorelbine-induced cell death.
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Affiliation(s)
- Avital Schwed-Gross
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hila Hamiel
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Gabriel P Faber
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Mor Angel
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Rakefet Ben-Yishay
- Oncology Institute, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Jennifer I C Benichou
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dana Ishay-Ronen
- Oncology Institute, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
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Aleshkina D, Iyyappan R, Lin CJ, Masek T, Pospisek M, Susor A. ncRNA BC1 influences translation in the oocyte. RNA Biol 2021; 18:1893-1904. [PMID: 33491548 PMCID: PMC8583082 DOI: 10.1080/15476286.2021.1880181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/17/2020] [Accepted: 01/15/2021] [Indexed: 01/06/2023] Open
Abstract
Regulation of translation is essential for the diverse biological processes involved in development. Particularly, mammalian oocyte development requires the precisely controlled translation of maternal transcripts to coordinate meiotic and early embryo progression while transcription is silent. It has been recently reported that key components of mRNA translation control are short and long noncoding RNAs (ncRNAs). We found that the ncRNABrain cytoplasmic 1 (BC1) has a role in the fully grown germinal vesicle (GV) mouse oocyte, where is highly expressed in the cytoplasm associated with polysomes. Overexpression of BC1 in GV oocyte leads to a minute decrease in global translation with a significant reduction of specific mRNA translation via interaction with the Fragile X Mental Retardation Protein (FMRP). BC1 performs a repressive role in translation only in the GV stage oocyte without forming FMRP or Poly(A) granules. In conclusion, BC1 acts as the translational repressor of specific mRNAs in the GV stage via its binding to a subset of mRNAs and physical interaction with FMRP. The results reported herein contribute to the understanding of the molecular mechanisms of developmental events connected with maternal mRNA translation.
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Affiliation(s)
- D. Aleshkina
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - R. Iyyappan
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Ch. J. Lin
- MRC Centre for Reproductive Health, The University of Edinburgh, Edinburgh, UK
| | - T. Masek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - M. Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - A. Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
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10
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Chalkiadaki K, Statoulla E, Markou M, Bellou S, Bagli E, Fotsis T, Murphy C, Gkogkas CG. Translational control in neurovascular brain development. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211088. [PMID: 34659781 PMCID: PMC8511748 DOI: 10.1098/rsos.211088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
The human brain carries out complex tasks and higher functions and is crucial for organismal survival, as it senses both intrinsic and extrinsic environments. Proper brain development relies on the orchestrated development of different precursor cells, which will give rise to the plethora of mature brain cell-types. Within this process, neuronal cells develop closely to and in coordination with vascular cells (endothelial cells (ECs), pericytes) in a bilateral communication process that relies on neuronal activity, attractive or repulsive guidance cues for both cell types and on tight-regulation of gene expression. Translational control is a master regulator of the gene-expression pathway and in particular for neuronal and ECs, it can be localized in developmentally relevant (axon growth cone, endothelial tip cell) and mature compartments (synapses, axons). Herein, we will review mechanisms of translational control relevant to brain development in neurons and ECs in health and disease.
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Affiliation(s)
- Kleanthi Chalkiadaki
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Elpida Statoulla
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Maria Markou
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Sofia Bellou
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Eleni Bagli
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Theodore Fotsis
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Carol Murphy
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Christos G. Gkogkas
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
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11
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Chua JP, De Calbiac H, Kabashi E, Barmada SJ. Autophagy and ALS: mechanistic insights and therapeutic implications. Autophagy 2021; 18:254-282. [PMID: 34057020 PMCID: PMC8942428 DOI: 10.1080/15548627.2021.1926656] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mechanisms of protein homeostasis are crucial for overseeing the clearance of misfolded and toxic proteins over the lifetime of an organism, thereby ensuring the health of neurons and other cells of the central nervous system. The highly conserved pathway of autophagy is particularly necessary for preventing and counteracting pathogenic insults that may lead to neurodegeneration. In line with this, mutations in genes that encode essential autophagy factors result in impaired autophagy and lead to neurodegenerative conditions such as amyotrophic lateral sclerosis (ALS). However, the mechanistic details underlying the neuroprotective role of autophagy, neuronal resistance to autophagy induction, and the neuron-specific effects of autophagy-impairing mutations remain incompletely defined. Further, the manner and extent to which non-cell autonomous effects of autophagy dysfunction contribute to ALS pathogenesis are not fully understood. Here, we review the current understanding of the interplay between autophagy and ALS pathogenesis by providing an overview of critical steps in the autophagy pathway, with special focus on pivotal factors impaired by ALS-causing mutations, their physiologic effects on autophagy in disease models, and the cell type-specific mechanisms regulating autophagy in non-neuronal cells which, when impaired, can contribute to neurodegeneration. This review thereby provides a framework not only to guide further investigations of neuronal autophagy but also to refine therapeutic strategies for ALS and related neurodegenerative diseases.Abbreviations: ALS: amyotrophic lateral sclerosis; Atg: autophagy-related; CHMP2B: charged multivesicular body protein 2B; DPR: dipeptide repeat; FTD: frontotemporal dementia; iPSC: induced pluripotent stem cell; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; PINK1: PTEN induced kinase 1; RNP: ribonuclear protein; sALS: sporadic ALS; SPHK1: sphingosine kinase 1; TARDBP/TDP-43: TAR DNA binding protein; TBK1: TANK-binding kinase 1; TFEB: transcription factor EB; ULK: unc-51 like autophagy activating kinase; UPR: unfolded protein response; UPS: ubiquitin-proteasome system; VCP: valosin containing protein.
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Affiliation(s)
- Jason P Chua
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
| | - Hortense De Calbiac
- Recherche translationnelle sur les maladies neurologiques, Institut Imagine, UMR-1163 INSERM et Université Paris Descartes, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Edor Kabashi
- Recherche translationnelle sur les maladies neurologiques, Institut Imagine, UMR-1163 INSERM et Université Paris Descartes, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
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12
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Ruan T, Zhang Y, Liu W, Li Y, Wang D, Du Z, Tao K, Wu C. Expression of DCP1a in gastric cancer and its biological function and mechanism in chemotherapy resistance in gastric cancer cells. Dig Liver Dis 2020; 52:1351-1358. [PMID: 32646734 DOI: 10.1016/j.dld.2020.06.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022]
Abstract
AIMS To detect the role of DCP1a in gastric cancer. To estimate the effect of DCP1a in gastric cancer cells on proliferation, invasion, migration and anti-drug behavior in vitro by down-regulating its expression. METHODS Using IHC staining and Western blot to check the expression of DCP1a in tissues and the cell lines. SGC7901 and BGC823 cells were transfected with DCP1a siRNA, and the expression of DCP1a protein and mRNA were detected. The cell proliferation rate was detected by MTT assay and plate cloning assay. Transwell assay was used to detect the change of cell metastasis. The inhibition rates of cells to chemotherapy were detected by MTT assay. And signal pathways were also detected. RESULTS The expression of DCP1a in cancer tissues is higher (p < 0.05), and higher expression of DCP1a is related to poor prognosis. After down-regulating the expression of DCP1a in cells, the proliferation rates, migration abilities and chemotherapy resistance decrease. We find that the expression of MRP-1 and the activation of AKT and STAT3 pathways might be involved in regulation. CONCLUSION The high expression of DCP1a might be associated with cancer development and prognosis. Down-regulating the expression of DCP1a will help to reduce chemotherapy resistance, which will help with further improvement of chemotherapy in gastric cancer.
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Affiliation(s)
- Tuo Ruan
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei, PR China
| | - Yazhi Zhang
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei, PR China
| | - Weizhen Liu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei, PR China
| | - Yuan Li
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei, PR China
| | - Dianshi Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei, PR China
| | - Zhouyuan Du
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei, PR China
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei, PR China.
| | - Chuanqing Wu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei, PR China.
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13
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Omer A, Patel D, Moran JL, Lian XJ, Di Marco S, Gallouzi IE. Autophagy and heat-shock response impair stress granule assembly during cellular senescence. Mech Ageing Dev 2020; 192:111382. [PMID: 33049246 DOI: 10.1016/j.mad.2020.111382] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/21/2020] [Accepted: 10/05/2020] [Indexed: 01/08/2023]
Abstract
Stress granules (SGs) are membraneless organelles formed in response to insult. These granules are related to pathological granules found in age-related neurogenerative diseases such as Parkinson's and Alzheimer's. Previously, we demonstrated that senescent cells, which accumulate with age, exposed to chronic oxidative stress, are unable to form SGs. Here, we show that the senescent cells' inability to form SGs correlates with an upregulation in both the heat-shock response and autophagy pathways, both of which are well-established promoters of SG disassembly. Our data also reveals that the knockdown of HSP70 and ATG5, important components of the heat-shock response and autophagy pathways, respectively, restores the number of SGs formed in senescent cells exposed to chronic oxidative stress. Surprisingly, under these conditions, the depletion of HSP70 or ATG5 did not affect the clearance of these SGs during their recovery from chronic stress. These data reveal that senescent cells possess a unique heat-shock and autophagy-dependent ability to impair the formation of SGs in response to chronic stress, thereby expanding the existing understanding of SG dynamics in senescent cells and their potential contribution to age-related neurodegenerative diseases.
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Affiliation(s)
- Amr Omer
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada.
| | - Devang Patel
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada
| | - Julian Lucas Moran
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada
| | - Xian Jin Lian
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada
| | - Sergio Di Marco
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada
| | - Imed-Eddine Gallouzi
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada.
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14
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Schieweck R, Ninkovic J, Kiebler MA. RNA-binding proteins balance brain function in health and disease. Physiol Rev 2020; 101:1309-1370. [PMID: 33000986 DOI: 10.1152/physrev.00047.2019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Posttranscriptional gene expression including splicing, RNA transport, translation, and RNA decay provides an important regulatory layer in many if not all molecular pathways. Research in the last decades has positioned RNA-binding proteins (RBPs) right in the center of posttranscriptional gene regulation. Here, we propose interdependent networks of RBPs to regulate complex pathways within the central nervous system (CNS). These are involved in multiple aspects of neuronal development and functioning, including higher cognition. Therefore, it is not sufficient to unravel the individual contribution of a single RBP and its consequences but rather to study and understand the tight interplay between different RBPs. In this review, we summarize recent findings in the field of RBP biology and discuss the complex interplay between different RBPs. Second, we emphasize the underlying dynamics within an RBP network and how this might regulate key processes such as neurogenesis, synaptic transmission, and synaptic plasticity. Importantly, we envision that dysfunction of specific RBPs could lead to perturbation within the RBP network. This would have direct and indirect (compensatory) effects in mRNA binding and translational control leading to global changes in cellular expression programs in general and in synaptic plasticity in particular. Therefore, we focus on RBP dysfunction and how this might cause neuropsychiatric and neurodegenerative disorders. Based on recent findings, we propose that alterations in the entire regulatory RBP network might account for phenotypic dysfunctions observed in complex diseases including neurodegeneration, epilepsy, and autism spectrum disorders.
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Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Jovica Ninkovic
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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15
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Hofmann S, Kedersha N, Anderson P, Ivanov P. Molecular mechanisms of stress granule assembly and disassembly. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118876. [PMID: 33007331 DOI: 10.1016/j.bbamcr.2020.118876] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 12/11/2022]
Abstract
Stress granules (SGs) are membrane-less ribonucleoprotein (RNP)-based cellular compartments that form in the cytoplasm of a cell upon exposure to various environmental stressors. SGs contain a large set of proteins, as well as mRNAs that have been stalled in translation as a result of stress-induced polysome disassembly. Despite the fact that SGs have been extensively studied for many years, their function is still not clear. They presumably help the cell to cope with the encountered stress, and facilitate the recovery process after stress removal upon which SGs disassemble. Aberrant formation of SGs and impaired SG disassembly majorly contribute to various pathological phenomena in cancer, viral infections, and neurodegeneration. The assembly of SGs is largely driven by liquid-liquid phase separation (LLPS), however, the molecular mechanisms behind that are not fully understood. Recent studies have proposed a novel mechanism for SG formation that involves the interplay of a large interaction network of mRNAs and proteins. Here, we review this novel concept of SG assembly, and discuss the current insights into SG disassembly.
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Affiliation(s)
- Sarah Hofmann
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nancy Kedersha
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paul Anderson
- Brigham and Women's Hospital, Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Pavel Ivanov
- Brigham and Women's Hospital, Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
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16
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Zhao D, Li J, Wang Y, Li X, Gao L, Cao H, Zheng SJ. Critical role for G3BP1 in infectious bursal disease virus (IBDV)-induced stress granule formation and viral replication. Vet Microbiol 2020; 248:108806. [PMID: 32827928 DOI: 10.1016/j.vetmic.2020.108806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/18/2020] [Indexed: 12/24/2022]
Abstract
Stress granules (SGs), complexes for mRNA storage, are formed in host cellular response to stress stimuli and play an important role in innate immune response. GTPase-activating protein (SH3 domain)-binding protein 1 (G3BP1) is a key component of SGs. However, whether IBDV infection induces SG formation in host cells and what role of G3BP1 plays in this process are unclear. We report here that IBDV infection initiated typical stress granule formation and enhanced G3BP1 expression in DF-1 cells. Our data show that knockdown of G3BP1 by RNAi markedly inhibited IBDV-induced SG formation and viral replication in DF-1 cells. Conversely, ectopic expression of G3BP1 enhanced IBDV-induced SG formation and significantly promoted IBDV replication in host cells. Thus, G3BP1 plays a critical role in IBDV-induced SG formation and viral replication, providing an important clue to elucidating how IBDV employs cellular SGs for its own benefits.
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Affiliation(s)
- Dianzheng Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jiaxin Li
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yongqiang Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiaoqi Li
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Li Gao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hong Cao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Shijun J Zheng
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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17
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Xu L, Liu T, Xiong X, Liu W, Yu Y, Cao J. AtC3H18L is a stop-codon read-through gene and encodes a novel non-tandem CCCH zinc-finger protein that can form cytoplasmic foci similar to mRNP granules. Biochem Biophys Res Commun 2020; 528:140-145. [PMID: 32451083 DOI: 10.1016/j.bbrc.2020.05.081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 11/18/2022]
Abstract
The membraneless messenger ribonucleoprotein (mRNP) granules, including processing bodies (PBs) and stress granules (SGs), are important cytoplasmic structures in eukaryotes that can participate in gene expression through mRNA regulation. It has been verified that mRNP granules are mainly composed of proteins and translation-repressed mRNAs. Here, we reported a stop-codon read-through gene, At3g52980, in plants for the first time. At3g52980 encodes a novel non-tandem CCCH zinc-finger (non-TZF) protein named AtC3H18-Like (AtC3H18L), which contains two putative RNA-binding domains. By using transient expression system, we showed that heat treatment can induce the aggregation of diffuse distributed AtC3H18L to form cytoplasmic foci, which were similar to PBs and SGs in morphology. Further analysis did find that AtC3H18L can co-localize with markers of PB and SG. The aggregation of AtC3H18L was closely related to the cytoskeleton, and AtC3H18L-foci were highly dynamic and can move frequently along cytoskeleton. Moreover, analysis in transgenic plants showed that AtC3H18L was specifically expressed in pollen and can form cytoplasmic foci without heat treatment. It will be fascinating in future studies to discover whether and how AtC3H18L affects pollen development by participating in the assembly of mRNP granules as a protein component, especially under heat stress.
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Affiliation(s)
- Liai Xu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
| | - Tingting Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
| | - Xingpeng Xiong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
| | - Weimiao Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
| | - Youjian Yu
- Department of Horticulture, College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, 311300, China.
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
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18
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Peña EJ, Heinlein M. Visualization of Transiently Expressed mRNA in Plants Using MS2. Methods Mol Biol 2020; 2166:103-120. [PMID: 32710405 DOI: 10.1007/978-1-0716-0712-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
RNA transport and localization are evolutionarily conserved processes that allow protein translation to occur at specific subcellular sites and thereby having fundamental roles in the determination of cell fates, embryonic patterning, asymmetric cell division, and cell polarity. In addition to localizing RNA molecules to specific subcellular sites, plants have the ability to exchange RNA molecules between cells through plasmodesmata (PD). Plant RNA viruses hijack the mechanisms of intracellular and intercellular RNA transport to establish localized replication centers within infected cells and then to disseminate their infectious genomes between cells and throughout the plant organism with the help of their movement proteins (MP). In this chapter, we describe the transient expression of the tobacco mosaic virus movement protein (TMV-MP) and the application of the MS2 system for the in vivo labeling of the MP-encoding mRNA. The MS2 method is based on the binding of the bacteriophage coat protein (CP) to its origin of assembly (OAS) in the phage RNA. Thus, to label a specific mRNA in vivo, a tandem repetition of a 19-nucleotide-long stem-loop (SL) sequence derived from the MS2 OAS sequence (MSL) is transcriptionally fused to the RNA under investigation. The RNA is detected by the co-expression of fluorescent protein-tagged MS2 CP (MCP), which binds to each of the MSL elements. In providing a detailed protocol for the in vivo visualization of TMV-MP mRNA tagged with the MS2 system in Nicotiana benthamiana epidermal cells, we describe (1) the specific DNA constructs, (2) Agrobacterium tumefaciens-mediated transfection for their transient expression in plants, and (3) imaging conditions required to obtain high-quality mRNA imaging data.
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Affiliation(s)
- Eduardo José Peña
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata CONICET, Fac. Cs. Exactas, U.N.L.P, La Plata, Argentina
| | - Manfred Heinlein
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France.
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19
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Rha AK, Das D, Taran O, Ke Y, Mehta AK, Lynn DG. Electrostatic Complementarity Drives Amyloid/Nucleic Acid Co‐Assembly. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907661] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Allisandra K. Rha
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Dibyendu Das
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Olga Taran
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Yonggang Ke
- Biomedical Engineering Emory and Georgia Institute of Technology Atlanta GA 30322 USA
| | - Anil K. Mehta
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
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20
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Rha AK, Das D, Taran O, Ke Y, Mehta AK, Lynn DG. Electrostatic Complementarity Drives Amyloid/Nucleic Acid Co-Assembly. Angew Chem Int Ed Engl 2019; 59:358-363. [PMID: 31617300 DOI: 10.1002/anie.201907661] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/11/2019] [Indexed: 12/20/2022]
Abstract
Proteinaceous plaques associated with neurodegenerative diseases contain many biopolymers including the polyanions glycosaminoglycans and nucleic acids. Polyanion-induced amyloid fibrillation has been implicated in disease etiology, but structural models for amyloid/nucleic acid co-assemblies remain limited. Here we constrain nucleic acid/peptide interactions with model peptides that exploit electrostatic complementarity and define a novel amyloid/nucleic acid co-assembly. The structure provides a model for nucleic acid/amyloid co-assembly as well as insight into the energetic determinants involved in templating amyloid assembly.
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Affiliation(s)
- Allisandra K Rha
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - Dibyendu Das
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - Olga Taran
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - Yonggang Ke
- Biomedical Engineering, Emory and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Anil K Mehta
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - David G Lynn
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
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Abstract
RNA localization mechanisms have been intensively studied and include localized protection of mRNA from degradation, diffusion-coupled local entrapment of mRNA, and directed transport of mRNAs along the cytoskeleton. While it is well understood how cells utilize these three mechanisms to organize mRNAs within the cytoplasm, a newly appreciated mechanism of RNA localization has emerged in recent years in which mRNAs phase-separate and form liquid-like droplets. mRNAs both contribute to condensation of proteins into liquid-like structures and are themselves regulated by being incorporated into membraneless organelles. This ability to condense into droplets is in many instances contributing to previously appreciated mRNA localization phenomena. Here we review how phase separation enables mRNAs to selectively and efficiently colocalize and be coregulated, allowing control of gene expression in time and space.
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Affiliation(s)
- Erin M Langdon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
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CNOT2 facilitates dengue virus infection via negatively modulating IFN-Independent Non-Canonical JAK/STAT pathway. Biochem Biophys Res Commun 2019; 515:403-409. [DOI: 10.1016/j.bbrc.2019.05.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 05/11/2019] [Indexed: 01/02/2023]
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Overexpression of mRNA-decapping enzyme 1a predicts disease-specific survival in malignant melanoma. Melanoma Res 2018; 28:30-36. [PMID: 29076924 DOI: 10.1097/cmr.0000000000000406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Our previous study identified that rs11551405 A allele located at the 3' UTR of mRNA-decapping enzyme 1a (DCP1A) was associated with an increased risk for malignant melanoma (MM). The aim of this study was to investigate whether that association is manifested at the DCP1A expression and whether an altered DCP1A expression can predict disease-specific survival (DSS) of MM patients. The DCP1A expression in specimens of 56 cases of primary MM (23 cases at TNM stage I-II and 33 cases at TNM stage III-IV) and 43 cases of benign nevi (BN) was measured by quantitative RT-PCR (qRT-PCR), immunohistochemistry, and western blotting. The levels of DCP1A expression and the clinical characteristics of the patients were recorded and compared, along with the DSS within the 3 years of follow-up. The average relative mRNA level of DCP1A was significantly (P=0.002) higher in the MM tissues (0.159±0.007) than that shown in the BN tissues (0.122±0.009). The DCP1A immunohistochemistry scores of MM samples (5.55±2.56) were significantly (P<0.001) higher than those of the BN samples (3.58±3.66). Tissue protein levels of DCP1A in MM (0.378±0.021) were much (P<0.05) higher than those in BN tissues (0.265±0.017). Higher DCP1A expression was significantly correlated with shorter DSS time in patients with MM (P<0.05). The multivariate Cox regression analysis revealed that DCP1A expression was an independent prognostic factor for DSS (hazard ratio=1.648, P=0.021). Elevation of DCP1A expression may be an epigenetic contributing factor for oncogenesis of MM, and high DCP1A level may predict an unfavorable prognosis for MM.
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FAM98A is localized to stress granules and associates with multiple stress granule-localized proteins. Mol Cell Biochem 2018; 451:107-115. [DOI: 10.1007/s11010-018-3397-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
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Wu C, Liu W, Ruan T, Zhu X, Tao K, Zhang W. Overexpression of mRNA-decapping enzyme 1a affects survival rate in colorectal carcinoma. Oncol Lett 2018; 16:1095-1100. [PMID: 29963186 DOI: 10.3892/ol.2018.8730] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 02/02/2018] [Indexed: 01/01/2023] Open
Abstract
Processing bodies (P-bodies) are one of the most well understood types of RNA granules, and are associated with a variety of diseases, including cancer. mRNA-decapping enzyme 1a (DCP1a), which may be used as a marker to analyze P-bodies, participates in the removal of the 5'-methylguanosine cap from eukaryotic mRNAs as a cofactor. The aim of the present study was to analyze the association between DCP1a expression and clinical features in colorectal carcinoma (CRC). The levels of DCP1a mRNA expression were detected by reverse transcription-quantitative polymerase chain reaction assay in carcinoma and non-carcinoma tissues from 75 patients, while the protein expression levels were evaluated by immunohistochemistry and western blotting. Additional associations between DCP1a expression and clinical characteristics were analyzed by χ2 test and Cox regression analysis. In the 75 cases, the levels of DCP1a mRNA and protein expression were increased in colorectal carcinoma tissues compared with non-carcinoma tissues. A high expression of DCP1a was significantly associated with lower survival rates in patients with CRC compared with patients with low DCP1a expression (P=0.001). Associations with depth of invasion (P=0.008), lymph node metastasis (P=0.001) and tumor node metastasis stage (P=0.001) were also observed. Additional Cox regression analysis revealed that the DCP1a expression (P=0.012) is an independent factor in survival rate. It was also identified that DCP1a may have high expression in colorectal carcinoma tissues and be associated with poor prognosis. This suggests that DCP1a may be a diagnostic marker or prognostic indicator to assist with patient assessments and therapies.
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Affiliation(s)
- Chuanqing Wu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Weizhen Liu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Tuo Ruan
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiaojie Zhu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Weikang Zhang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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Scutenaire J, Deragon JM, Jean V, Benhamed M, Raynaud C, Favory JJ, Merret R, Bousquet-Antonelli C. The YTH Domain Protein ECT2 Is an m 6A Reader Required for Normal Trichome Branching in Arabidopsis. THE PLANT CELL 2018; 30:986-1005. [PMID: 29618631 PMCID: PMC6002185 DOI: 10.1105/tpc.17.00854] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/01/2018] [Accepted: 04/04/2018] [Indexed: 05/14/2023]
Abstract
Methylations at position N6 of internal adenosines (m6As) are the most abundant and widespread mRNA modifications. These modifications play crucial roles in reproduction, growth, and development by controlling gene expression patterns at the posttranscriptional level. Their function is decoded by readers that share the YTH domain, which forms a hydrophobic pocket that directly accommodates the m6A residues. While the physiological and molecular functions of YTH readers have been extensively studied in animals, little is known about plant readers, even though m6As are crucial for plant survival and development. Viridiplantae contains high numbers of YTH domain proteins. Here, we performed comprehensive evolutionary analysis of YTH domain proteins and demonstrated that they are highly likely to be actual readers with redundant as well as specific functions. We also show that the ECT2 protein from Arabidopsis thaliana binds to m6A-containing RNAs in vivo and that this property relies on the m6A binding pocket carried by its YTH domain. ECT2 is cytoplasmic and relocates to stress granules upon heat exposure, suggesting that it controls mRNA fate in the cytosol. Finally, we demonstrate that ECT2 acts to decode the m6A signal in the trichome and is required for their normal branching through controlling their ploidy levels.
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Affiliation(s)
- Jérémy Scutenaire
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Jean-Marc Deragon
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Institut Universitaire de France, 75231 Paris Cedex 05, France
| | - Viviane Jean
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Moussa Benhamed
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Cécile Raynaud
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Jean-Jacques Favory
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Rémy Merret
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Cécile Bousquet-Antonelli
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
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IL-17-receptor-associated adaptor Act1 directly stabilizes mRNAs to mediate IL-17 inflammatory signaling. Nat Immunol 2018; 19:354-365. [PMID: 29563620 PMCID: PMC6082628 DOI: 10.1038/s41590-018-0071-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 02/16/2018] [Indexed: 12/15/2022]
Abstract
Mechanisms that degrade inflammatory mRNAs are well-known, however
stabilizing mechanisms are poorly understood. Here we show that Act1, an
interleukin-17 (IL-17) receptor complex adaptor, binds and stabilizes mRNAs
encoding key inflammatory proteins. The Act1 SEFIR domain binds a stem-loop
structure, SBE (SEFIR-binding element), in the inflammatory chemokine
Cxcl1 3’ UTR. mRNA-bound Act1 directs formation of
three compartmentally-distinct protein-RNA complexes (RNPs) that regulate three
disparate events in inflammatory mRNA metabolism: preventing mRNA decay in the
nucleus, inhibiting mRNA decapping in P-bodies, and promoting translation. SBE
RNA aptamers reduced IL-17-mediated mRNA stabilization in
vitro, IL-17-induced skin inflammation and airway inflammation in a
mouse asthma model, providing a therapeutic strategy for autoimmune diseases.
These results reveal a network in which Act1 assembles RNPs on the 3’
UTRs of select mRNAs to control receptor-mediated mRNA stabilization and
translation during inflammation.
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Taran O, Chen C, Omosun TO, Hsieh MC, Rha A, Goodwin JT, Mehta AK, Grover MA, Lynn DG. Expanding the informational chemistries of life: peptide/RNA networks. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0356. [PMID: 29133453 DOI: 10.1098/rsta.2016.0356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
- Olga Taran
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Chenrui Chen
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Tolulope O Omosun
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Ming-Chien Hsieh
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Allisandra Rha
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Jay T Goodwin
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Anil K Mehta
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Martha A Grover
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - David G Lynn
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
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El Zowalaty AE, Li R, Zheng Y, Lydon JP, DeMayo FJ, Ye X. Deletion of RhoA in Progesterone Receptor-Expressing Cells Leads to Luteal Insufficiency and Infertility in Female Mice. Endocrinology 2017; 158:2168-2178. [PMID: 28498971 PMCID: PMC5505209 DOI: 10.1210/en.2016-1796] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 05/08/2017] [Indexed: 12/22/2022]
Abstract
Ras homolog gene family, member A (RhoA) is widely expressed throughout the female reproductive system. To assess its role in progesterone receptor-expressing cells, we generated RhoA conditional knockout mice RhoAd/d (RhoAf/f-Pgr-Cre+/-). RhoAd/d female mice had comparable mating activity, serum luteinizing hormone, prolactin, and estradiol levels and ovulation with control but were infertile with progesterone insufficiency, indicating impaired steroidogenesis in RhoAd/d corpus luteum (CL). RhoA was highly expressed in wild-type luteal cells and conditionally deleted in RhoAd/d CL. Gestation day 3.5 (D3.5) RhoAd/d ovaries had reduced numbers of CL, less defined corpus luteal cord formation, and disorganized CL collagen IV staining. RhoAd/d CL had lipid droplet and free cholesterol accumulation, indicating the availability of cholesterol for steroidogenesis, but disorganized β-actin and vimentin staining, indicating disrupted cytoskeleton integrity. Cytoskeleton is important for cytoplasmic cholesterol movement to mitochondria and for regulating mitochondria. Dramatically reduced expression of mitochondrial markers heat shock protein 60 (HSP60), voltage-dependent anion channel, and StAR was detected in RhoAd/d CL. StAR carries out the rate-limiting step of steroidogenesis. StAR messenger RNA expression was reduced in RU486-treated D3.5 wild-type CL and tended to be induced in progesterone-treated D3.5 RhoAd/d CL, with parallel changes of HSP60 expression. These data demonstrated the in vivo function of RhoA in CL luteal cell cytoskeleton integrity, cholesterol transport, StAR expression, and progesterone synthesis, and a positive feedback on StAR expression in CL by progesterone signaling. These findings provide insights into mechanisms of progesterone insufficiency.
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Affiliation(s)
- Ahmed E. El Zowalaty
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia 30602
| | - Rong Li
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia 30602
| | - Yi Zheng
- Division of Experimental Hematology and Cancer Biology, Children’s Hospital Research Foundation, Cincinnati, Ohio 45229
| | - John P. Lydon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Francesco J. DeMayo
- Reproductive and Developmental Biology Laboratory/Pregnancy and Female Reproduction Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Xiaoqin Ye
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia 30602
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Wang X, Chang L, Wang H, Su A, Wu Z. Dcp1a and GW182 Induce Distinct Cellular Aggregates and Have Different Effects on microRNA Pathway. DNA Cell Biol 2017; 36:565-570. [DOI: 10.1089/dna.2017.3633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Xiaohui Wang
- Department of Hematology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, People's Republic of China
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Liang Chang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Huanru Wang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Airong Su
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
- State Key Lab of Analytical Chemistry for Life Science, Nanjing University, Nanjing, People's Republic of China
- Jiangsu Laboratory for Molecular Medicines, Nanjing University, Nanjing, People's Republic of China
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32
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Mihailovic MK, Chen A, Gonzalez-Rivera JC, Contreras LM. Defective Ribonucleoproteins, Mistakes in RNA Processing, and Diseases. Biochemistry 2017; 56:1367-1382. [PMID: 28206738 DOI: 10.1021/acs.biochem.6b01134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribonucleoproteins (RNPs) are vital to many cellular events. To this end, many neurodegenerative diseases and cancers have been linked to RNP malfunction, particularly as this relates to defective processing of cellular RNA. The connection of RNPs and diseases has also propagated a shift of focus onto RNA targeting from traditional protein targeting treatments. However, therapeutic development in this area has been limited by incomplete molecular insight into the specific contributions of RNPs to disease. This review outlines the role of several RNPs in diseases, focusing on molecular defects in processes that affect proper RNA handling in the cell. This work also evaluates the contributions of recently developed methods to understanding RNP association and function. We review progress in this area by focusing on molecular malfunctions of RNPs associated with the onset and progression of several neurodegenerative diseases and cancer and conclude with a brief discussion of RNA-based therapeutic efforts.
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Affiliation(s)
- Mia K Mihailovic
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Angela Chen
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Juan C Gonzalez-Rivera
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
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Nikolic J, Civas A, Lama Z, Lagaudrière-Gesbert C, Blondel D. Rabies Virus Infection Induces the Formation of Stress Granules Closely Connected to the Viral Factories. PLoS Pathog 2016; 12:e1005942. [PMID: 27749929 PMCID: PMC5066959 DOI: 10.1371/journal.ppat.1005942] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022] Open
Abstract
Stress granules (SGs) are membrane-less dynamic structures consisting of mRNA and protein aggregates that form rapidly in response to a wide range of environmental cellular stresses and viral infections. They act as storage sites for translationally silenced mRNAs under stress conditions. During viral infection, SG formation results in the modulation of innate antiviral immune responses, and several viruses have the ability to either promote or prevent SG assembly. Here, we show that rabies virus (RABV) induces SG formation in infected cells, as revealed by the detection of SG-marker proteins Ras GTPase-activating protein-binding protein 1 (G3BP1), T-cell intracellular antigen 1 (TIA-1) and poly(A)-binding protein (PABP) in the RNA granules formed during viral infection. As shown by live cell imaging, RABV-induced SGs are highly dynamic structures that increase in number, grow in size by fusion events, and undergo assembly/disassembly cycles. Some SGs localize in close proximity to cytoplasmic viral factories, known as Negri bodies (NBs). Three dimensional reconstructions reveal that both structures remain distinct even when they are in close contact. In addition, viral mRNAs synthesized in NBs accumulate in the SGs during viral infection, revealing material exchange between both compartments. Although RABV-induced SG formation is not affected in MEFs lacking TIA-1, TIA-1 depletion promotes viral translation which results in an increase of viral replication indicating that TIA-1 has an antiviral effect. Inhibition of PKR expression significantly prevents RABV-SG formation and favors viral replication by increasing viral translation. This is correlated with a drastic inhibition of IFN-B gene expression indicating that SGs likely mediate an antiviral response which is however not sufficient to fully counteract RABV infection.
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Affiliation(s)
- Jovan Nikolic
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ahmet Civas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Zoé Lama
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cécile Lagaudrière-Gesbert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Danielle Blondel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
- * E-mail:
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Mugler CF, Hondele M, Heinrich S, Sachdev R, Vallotton P, Koek AY, Chan LY, Weis K. ATPase activity of the DEAD-box protein Dhh1 controls processing body formation. eLife 2016; 5. [PMID: 27692063 PMCID: PMC5096884 DOI: 10.7554/elife.18746] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/28/2016] [Indexed: 12/22/2022] Open
Abstract
Translational repression and mRNA degradation are critical mechanisms of posttranscriptional gene regulation that help cells respond to internal and external cues. In response to certain stress conditions, many mRNA decay factors are enriched in processing bodies (PBs), cellular structures involved in degradation and/or storage of mRNAs. Yet, how cells regulate assembly and disassembly of PBs remains poorly understood. Here, we show that in budding yeast, mutations in the DEAD-box ATPase Dhh1 that prevent ATP hydrolysis, or that affect the interaction between Dhh1 and Not1, the central scaffold of the CCR4-NOT complex and an activator of the Dhh1 ATPase, prevent PB disassembly in vivo. Intriguingly, this process can be recapitulated in vitro, since recombinant Dhh1 and RNA, in the presence of ATP, phase-separate into liquid droplets that rapidly dissolve upon addition of Not1. Our results identify the ATPase activity of Dhh1 as a critical regulator of PB formation. DOI:http://dx.doi.org/10.7554/eLife.18746.001 Most cells and organisms live in changeable environments. Adapting to environmental changes means that organisms must quickly alter which of their genes they express. Varying which genes are switched on or off is not enough; cells must also degrade existing messenger RNAs (or mRNAs for short), which contain the genetic instructions of the previously active genes. Therefore, cells must tightly regulate the machinery needed to degrade mRNAs. When Baker’s yeast (also known as budding yeast) cells experience certain stressful conditions, the proteins that break down mRNAs localize into specific structures inside the cell known as ‘processing bodies’. These structures are found in many other organisms across evolution, from yeast to human. Processing bodies also form in a variety of biological contexts, such as in nerve cells and developing embryos. Still, why cells form processing bodies, and how their assembly is regulated, is not well understood. One essential component of processing bodies is an enzyme called Dhh1. This enzyme has been conserved throughout evolution and is known to promote the decay of mRNAs as well as to repress their translation into proteins. Now, Mugler, Hondele et al. show that Dhh1’s must break down molecules of the energy carrier ATP (referred to as its “ATPase activity”) in order to regulate the dynamic nature of processing bodies. Mutant Dhh1 proteins that lack ATPase activity form permanent processing bodies in non-stressed yeast cells. This shows that that the breakdown of ATP by Dhh1 is required for the disassembly of processing bodies. Similar results were seen for mutant Dhh1 proteins that cannot interact with Not1, a protein which enhances the ATPase activity of Dhh1. Next Mugler, Hondele et al. mixed purified Dhh1 with ATP and RNA molecules and saw that the mixture underwent a “liquid-liquid phase separation” and formed observable granules, similar to oil droplets in water. These granules dissolved when Not1 was added to stimulate the Dhh1 enzyme to turnover ATP. This showed that several important biochemical and biophysical aspects of processing bodies seen within living cells could be recreated outside of a cell. Armed with a greater understanding of the rules that govern the formation of processing bodies, future work can now address how important processing bodies are for regulating gene expression. Another challenge for the future will be to examine the specific roles that processing bodies play in yeast and other cells, like human egg cells or nerve cells. DOI:http://dx.doi.org/10.7554/eLife.18746.002
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Affiliation(s)
| | | | | | | | | | - Adriana Y Koek
- University of California, Berkeley, Berkeley, United States
| | - Leon Y Chan
- University of California, Berkeley, Berkeley, United States
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Kedersha N, Panas MD, Achorn CA, Lyons S, Tisdale S, Hickman T, Thomas M, Lieberman J, McInerney GM, Ivanov P, Anderson P. G3BP-Caprin1-USP10 complexes mediate stress granule condensation and associate with 40S subunits. J Cell Biol 2016; 212:845-60. [PMID: 27022092 PMCID: PMC4810302 DOI: 10.1083/jcb.201508028] [Citation(s) in RCA: 399] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/17/2016] [Indexed: 12/11/2022] Open
Abstract
Stress granule condensation (SGC) of translationally arrested mRNAs requires G3BP, and G3BP-mediated SGC is inhibited by serine 149 phosphorylation, regulated by mutually exclusive binding of Caprin1 and USP10, and requires its RGG region for SGC and for interactions with 40S ribosomal subunits. Mammalian stress granules (SGs) contain stalled translation preinitiation complexes that are assembled into discrete granules by specific RNA-binding proteins such as G3BP. We now show that cells lacking both G3BP1 and G3BP2 cannot form SGs in response to eukaryotic initiation factor 2α phosphorylation or eIF4A inhibition, but are still SG-competent when challenged with severe heat or osmotic stress. Rescue experiments using G3BP1 mutants show that phosphomimetic G3BP1-S149E fails to rescue SG formation, whereas G3BP1-F33W, a mutant unable to bind G3BP partner proteins Caprin1 or USP10, rescues SG formation. Caprin1/USP10 binding to G3BP is mutually exclusive: Caprin binding promotes, but USP10 binding inhibits, SG formation. G3BP interacts with 40S ribosomal subunits through its RGG motif, which is also required for G3BP-mediated SG formation. We propose that G3BP mediates the condensation of SGs by shifting between two different states that are controlled by the phosphorylation of S149 and by binding to Caprin1 or USP10.
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Affiliation(s)
- Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Marc D Panas
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Christopher A Achorn
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Shawn Lyons
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Sarah Tisdale
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Tyler Hickman
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Marshall Thomas
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115 The Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
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The C-Terminal RGG Domain of Human Lsm4 Promotes Processing Body Formation Stimulated by Arginine Dimethylation. Mol Cell Biol 2016; 36:2226-35. [PMID: 27247266 DOI: 10.1128/mcb.01102-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/23/2016] [Indexed: 12/31/2022] Open
Abstract
Processing bodies (PBs) are conserved cytoplasmic aggregations of translationally repressed mRNAs assembled with mRNA decay factors. The aggregation of mRNA-protein (mRNP) complexes into PBs involves interactions between low-complexity regions of protein components of the mRNPs. In Saccharomyces cerevisiae, the carboxy (C)-terminal Q/N-rich domain of the Lsm4 subunit of the Lsm1-7 complex plays an important role in PB formation, but the C-terminal domain of Lsm4 in most eukaryotes is an RGG domain rather than Q/N rich. Here we show that the Lsm4 RGG domain promotes PB accumulation in human cells and that symmetric dimethylation of arginines within the RGG domain stimulates this process. A mutant Lsm4 protein lacking the RGG domain failed to rescue PB formation in cells depleted of endogenous Lsm4, although this mutant protein retained the ability to assemble with Lsm1-7, associate with decapping factors, and promote mRNA decay and translational repression. Mutation of the symmetrically dimethylated arginines within the RGG domain impaired the ability of Lsm4 to promote PB accumulation. Depletion of PRMT5, the primary protein arginine methyltransferase responsible for symmetric arginine dimethylation, including Lsm4, resulted in loss of PBs. We also uncovered the histone acetyltransferase 1 (HAT1)-RBBP7 lysine acetylase complex as an interaction partner of the Lsm4 RGG domain but found no evidence of a role for this complex in PB metabolism. Together, our findings suggest a stimulatory role for posttranslational modifications in PB accumulation and raise the possibility that mRNP dynamics are posttranslationally regulated.
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Bowden HA, Dormann D. Altered mRNP granule dynamics in FTLD pathogenesis. J Neurochem 2016; 138 Suppl 1:112-33. [PMID: 26938019 DOI: 10.1111/jnc.13601] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/13/2022]
Abstract
In neurons, RNA-binding proteins (RBPs) play a key role in post-transcriptional gene regulation, for example alternative splicing, mRNA localization in neurites and local translation upon synaptic stimulation. There is increasing evidence that defective or mislocalized RBPs - and consequently altered mRNA processing - lead to neuronal dysfunction and cause neurodegeneration, including frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Cytosolic RBP aggregates containing TAR DNA-binding protein of 43 kDa (TDP-43) or fused in sarcoma (FUS) are a common hallmark of both disorders. There is mounting evidence that translationally silent mRNP granules, such as stress granules or transport granules, play an important role in the formation of these RBP aggregates. These granules are thought to be 'catalytic convertors' of RBP aggregation by providing a high local concentration of RBPs. As recently shown in vitro, RBPs that contain a so-called low-complexity domain start to 'solidify' and eventually aggregate at high protein concentrations. The same may happen in mRNP granules in vivo, leading to 'solidified' granules that lose their dynamic properties and ability to fulfill their physiological functions. This may result in a disturbed stress response, altered mRNA transport and local translation, and formation of pathological TDP-43 or FUS aggregates, all of which may contribute to neuronal dysfunction and neurodegeneration. Here, we discuss the general functional properties of these mRNP granules, how their dynamics may be disrupted in frontotemporal lobar degeneration/amyotrophic lateral sclerosis, for example by loss or gain of function of TDP-43 and FUS, and how this may contribute to the development of RBP aggregates and neurotoxicity. In this review, we discuss how dynamic mRNP granules, such as stress granules or neuronal transport granules, may be converted into pathological aggregates containing misfolded RNA-binding proteins (RBPs), such as TDP-43 and FUS. Abnormal interactions between low-complexity domains in RBPs may cause dynamic mRNP granules to solidify and become dysfunctional. This may result in a disturbed stress response, altered mRNA transport and local translation, as well as RBP aggregation, all of which may contribute to neuronal dysfunction and neurodegeneration.
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Affiliation(s)
- Hilary A Bowden
- Graduate School of Systemic Neurosciences (GSN), Planegg-Martinsried, Germany
| | - Dorothee Dormann
- BioMedical Center (BMC), Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,Graduate School of Systemic Neurosciences (GSN), Planegg-Martinsried, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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38
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Järvelin AI, Noerenberg M, Davis I, Castello A. The new (dis)order in RNA regulation. Cell Commun Signal 2016; 14:9. [PMID: 27048167 PMCID: PMC4822317 DOI: 10.1186/s12964-016-0132-3] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/21/2016] [Indexed: 02/03/2023] Open
Abstract
RNA-binding proteins play a key role in the regulation of all aspects of RNA metabolism, from the synthesis of RNA to its decay. Protein-RNA interactions have been thought to be mostly mediated by canonical RNA-binding domains that form stable secondary and tertiary structures. However, a number of pioneering studies over the past decades, together with recent proteome-wide data, have challenged this view, revealing surprising roles for intrinsically disordered protein regions in RNA binding. Here, we discuss how disordered protein regions can mediate protein-RNA interactions, conceptually grouping these regions into RS-rich, RG-rich, and other basic sequences, that can mediate both specific and non-specific interactions with RNA. Disordered regions can also influence RNA metabolism through protein aggregation and hydrogel formation. Importantly, protein-RNA interactions mediated by disordered regions can influence nearly all aspects of co- and post-transcriptional RNA processes and, consequently, their disruption can cause disease. Despite growing interest in disordered protein regions and their roles in RNA biology, their mechanisms of binding, regulation, and physiological consequences remain poorly understood. In the coming years, the study of these unorthodox interactions will yield important insights into RNA regulation in cellular homeostasis and disease.
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Affiliation(s)
- Aino I. Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Marko Noerenberg
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
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Abstract
Messenger ribonucleoprotein (mRNP) granules are dynamic, self-assembling structures that harbor non-translating mRNAs bound by various proteins that regulate mRNA translation, localization, and turnover. Their importance in gene expression regulation is far reaching, ranging from precise spatial-temporal control of mRNAs that drive developmental programs in oocytes and embryos, to similarly exquisite control of mRNAs in neurons that underpin synaptic plasticity, and thus, memory formation. Analysis of mRNP granules in their various contexts has revealed common themes of assembly, disassembly, and modes of mRNA regulation, yet new studies continue to reveal unexpected and important findings, such as links between aberrant mRNP granule assembly and neurodegenerative disease. Continued study of these enigmatic structures thus promises fascinating new insights into cellular function, and may also suggest novel therapeutic strategies in various disease states.
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Affiliation(s)
- J Ross Buchan
- a Department of Molecular and Cellular Biology ; University of Arizona ; Tucson , AZ USA
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40
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Wan D, Zhang ZC, Zhang X, Li Q, Han J. X chromosome-linked intellectual disability protein PQBP1 associates with and regulates the translation of specific mRNAs. Hum Mol Genet 2015; 24:4599-614. [DOI: 10.1093/hmg/ddv191] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/19/2015] [Indexed: 01/08/2023] Open
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Pérez-Vilaró G, Fernández-Carrillo C, Mensa L, Miquel R, Sanjuan X, Forns X, Pérez-del-Pulgar S, Díez J. Hepatitis C virus infection inhibits P-body granule formation in human livers. J Hepatol 2015; 62:785-90. [PMID: 25463546 DOI: 10.1016/j.jhep.2014.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/28/2014] [Accepted: 11/06/2014] [Indexed: 12/04/2022]
Abstract
BACKGROUND & AIMS Decoding the myriad of interactions that hepatitis C virus (HCV) establishes with infected cells is mandatory to obtain a complete understanding of HCV biology and its associated pathogenesis. We and others have previously found that HCV infection disrupts the formation of P-bodies in cell culture. These are cytoplasmic RNA granules with key roles in post-transcriptional regulation of gene expression. Therefore, P-body disruption might have consequences beyond viral propagation. However, whether P-body disruption occurs also in vivo is unknown. Aim of this study was to address this important issue. METHODS Formalin-fixed paraffin-embedded liver biopsies from four groups of patients (healthy donors, patients with non-virus related liver inflammation, HCV- and HBV-infected patients) were immunostained to detect DDX6 and Dcp1, two core P-body components. Changes in the localization of these proteins were assessed by confocal microscopy. RESULTS HCV specifically inhibited P-body formation in hepatocytes from human livers regardless of viral genotype, inflammation grade or whether the infection was recent or long established. Importantly, this alteration was reversed once HCV was eliminated by therapy. Furthermore, we observed in vivo an unexpected heterogeneity in P-body composition, which might reflect functional specializations. CONCLUSIONS This is the first comprehensive in vivo P-body analysis that links a pathogenic condition to P-body alterations. Because of their role in gene expression, the alteration of P-bodies should be further studied to understand fully complex HCV-associated pathologies.
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Affiliation(s)
| | | | - Laura Mensa
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Rosa Miquel
- Pathology Department, Hospital Clínic, Barcelona, Spain
| | - Xavier Sanjuan
- Scientific and Technical Services, Universitat Pompeu Fabra, Barcelona, Spain; Advanced Light Microscopy Unit, Center for Genomic Regulation, Barcelona, Spain
| | - Xavier Forns
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Barcelona, Spain
| | | | - Juana Díez
- Molecular Virology, Universitat Pompeu Fabra, Barcelona, Spain.
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42
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Fontana F, Siva K, Denti MA. A network of RNA and protein interactions in Fronto Temporal Dementia. Front Mol Neurosci 2015; 8:9. [PMID: 25852467 PMCID: PMC4365750 DOI: 10.3389/fnmol.2015.00009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 02/25/2015] [Indexed: 12/12/2022] Open
Abstract
Frontotemporal dementia (FTD) is a neurodegenerative disorder characterized by degeneration of the fronto temporal lobes and abnormal protein inclusions. It exhibits a broad clinicopathological spectrum and has been linked to mutations in seven different genes. We will provide a picture, which connects the products of these genes, albeit diverse in nature and function, in a network. Despite the paucity of information available for some of these genes, we believe that RNA processing and post-transcriptional regulation of gene expression might constitute a common theme in the network. Recent studies have unraveled the role of mutations affecting the functions of RNA binding proteins and regulation of microRNAs. This review will combine all the recent findings on genes involved in the pathogenesis of FTD, highlighting the importance of a common network of interactions in order to study and decipher the heterogeneous clinical manifestations associated with FTD. This approach could be helpful for the research of potential therapeutic strategies.
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Affiliation(s)
- Francesca Fontana
- Laboratory of RNA Biology and Biotechnology, Centre for Integrative Biology, University of TrentoTrento, Italy
| | - Kavitha Siva
- Laboratory of RNA Biology and Biotechnology, Centre for Integrative Biology, University of TrentoTrento, Italy
| | - Michela A. Denti
- Laboratory of RNA Biology and Biotechnology, Centre for Integrative Biology, University of TrentoTrento, Italy
- CNR, Institute of NeurosciencePadua, Italy
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43
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Melemedjian OK, Khoutorsky A. Translational control of chronic pain. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 131:185-213. [PMID: 25744674 DOI: 10.1016/bs.pmbts.2014.11.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pain is a crucial physiological response to injury and pathologies. The development and maintenance of pain requires the expression of novel genes. The expression of such genes occurs in highly regulated and orchestrated manner where protein translation provides an exquisite temporal and spatial fidelity within the axons and dendrites of neurons. Signaling pathways that regulate local translation are activated by cytokines, neurotrophic factors, or neurotransmitters, which are released either due to tissue damage or neuronal activity. In recent years, the ERK and mTOR pathways have been demonstrated to be central in regulating local translation in neurons of both the peripheral and central nervous systems in diverse models of chronic pain. The ERK and mTOR pathways converge onto the cap-dependent translational machinery that regulates genes essential for the development of nociceptive sensitization. Moreover, inhibition of these pathways has proved to be effective in normalizing the biochemical changes and the associated pain in various preclinical models.
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Affiliation(s)
- Ohannes K Melemedjian
- Department of Neural and Pain Sciences, School of Dentistry, University of Maryland, Baltimore, Maryland, USA.
| | - Arkady Khoutorsky
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Quebec, Canada
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44
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Jung H, Gkogkas CG, Sonenberg N, Holt CE. Remote control of gene function by local translation. Cell 2014; 157:26-40. [PMID: 24679524 PMCID: PMC3988848 DOI: 10.1016/j.cell.2014.03.005] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/04/2014] [Accepted: 03/04/2014] [Indexed: 12/12/2022]
Abstract
The subcellular position of a protein is a key determinant of its function. Mounting evidence indicates that RNA localization, where specific mRNAs are transported subcellularly and subsequently translated in response to localized signals, is an evolutionarily conserved mechanism to control protein localization. On-site synthesis confers novel signaling properties to a protein and helps to maintain local proteome homeostasis. Local translation plays particularly important roles in distal neuronal compartments, and dysregulated RNA localization and translation cause defects in neuronal wiring and survival. Here, we discuss key findings in this area and possible implications of this adaptable and swift mechanism for spatial control of gene function.
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Affiliation(s)
- Hosung Jung
- Department of Anatomy, Brain Research Institute, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, South Korea
| | - Christos G Gkogkas
- Patrick Wild Centre, Centre for Integrative Physiology, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada.
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, Anatomy Building, Downing Street, University of Cambridge, Cambridge CB2 3DY, UK.
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45
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Jedrusik-Bode M. C. elegans sirtuin SIR-2.4 and its mammalian homolog SIRT6 in stress response. WORM 2014; 3:e29102. [PMID: 26442197 DOI: 10.4161/worm.29102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/26/2014] [Accepted: 05/02/2014] [Indexed: 01/09/2023]
Abstract
Stress is a significant life event. The immediate response to stress is critical for survival. In organisms ranging from the unicellular Saccharomyces cerevisiae to protozoa (Trypanosoma brucei) and metazoan (such as Caenorhabditis elegans, Homo sapiens) stress response leads to the formation of cytoplasmic RNA-protein complexes referred to as stress granules (SGs). SGs regulate cell survival during stress by the sequestration of the signaling molecules implicated in apoptosis. They are a transient place of messenger ribonucleoproteins (mRNPs) remodeling for storage, degradation, or reinitiation of translation during stress and recovery from stress. Recently, we have identified chromatin factor, the sirtuin C. elegans SIR-2.4 variant and its mammalian homolog SIRT6 as a regulator of SGs formation. SIRT6 is highly conserved NAD(+)-dependent lysine deacetylase and ADP-ribosyltransferase impacting longevity, metabolism, and cancer. We observed that the cellular formation of SGs by SIRT6 or SIR-2.4 was linked with the cell viability or C. elegans survival and was dependent on SIRT6 enzymatic activity. Here, we discuss how SIR-2.4/SIRT6 influences SGs formation and stress response. We suggest possible mechanisms for such an unanticipated function of a chromatin regulatory factor SIRT6 in assembly of stress granules and cellular stress resistance.
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Affiliation(s)
- Monika Jedrusik-Bode
- Max Planck Institute for Biophysical Chemistry; Epigenetics in C elegans group; Göttingen, Germany
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46
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47
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Gao X, Shi X, Fu X, Ge L, Zhang Y, Su C, Yang X, Silvennoinen O, Yao Z, He J, Wei M, Yang J. Human Tudor staphylococcal nuclease (Tudor-SN) protein modulates the kinetics of AGTR1-3'UTR granule formation. FEBS Lett 2014; 588:2154-61. [PMID: 24815690 DOI: 10.1016/j.febslet.2014.04.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/17/2014] [Accepted: 04/25/2014] [Indexed: 10/25/2022]
Abstract
Human Tudor staphylococcal nuclease (Tudor-SN) interacts with the G3BP protein and is recruited into stress granules (SGs), the main type of discrete RNA-containing cytoplasmic foci structure that is formed under stress conditions. Here, we further demonstrate that Tudor-SN binds and co-localizes with AGTR1-3'UTR (3'-untranslated region of angiotensin II receptor, type 1 mRNA) into SG. Tudor-SN plays an important role in the assembly of AGTR1-3'UTR granules. Moreover, endogenous Tudor-SN knockdown can decrease the recovery kinetics of AGTR1-3'UTR granules. Collectively, our data indicate that Tudor-SN modulates the kinetics of AGTR1-3'UTR granule formation, which provides an additional biological role of Tudor-SN in RNA metabolism during stress.
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Affiliation(s)
- Xingjie Gao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Xuebin Shi
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Xue Fu
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Lin Ge
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Yi Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Chao Su
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Xi Yang
- Department of Immunology, University of Manitoba, 471 Apotex Centre, 750 McDermot Avenue, Winnipeg R3E 0T5, Canada
| | - Olli Silvennoinen
- Institute of Medical Technology, University of Tampere, Tampere University Hospital, Biokatu 8, FI-33014 Tampere, Finland
| | - Zhi Yao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Jinyan He
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Minxin Wei
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin 300070, China.
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China.
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48
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Ostareck DH, Naarmann-de Vries IS, Ostareck-Lederer A. DDX6 and its orthologs as modulators of cellular and viral RNA expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:659-78. [PMID: 24788243 DOI: 10.1002/wrna.1237] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/19/2014] [Accepted: 03/21/2014] [Indexed: 12/21/2022]
Abstract
DDX6 (Rck/p54), a member of the DEAD-box family of helicases, is highly conserved from unicellular eukaryotes to vertebrates. Functions of DDX6 and its orthologs in dynamic ribonucleoproteins contribute to global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay during development and differentiation in the germline and somatic cells. Its role in pathways that promote mRNA-specific alternative translation initiation has been shown to be linked to cellular homeostasis, deregulated tissue development, and the control of gene expression in RNA viruses. Recently, DDX6 was found to participate in mRNA regulation mediated by miRNA-mediated silencing. DDX6 and its orthologs have versatile functions in mRNA metabolism, which characterize them as important post-transcriptional regulators of gene expression.
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Affiliation(s)
- Dirk H Ostareck
- Experimental Research Unit, Department of Intensive Care and Intermediate Care, University Hospital, RWTH Aachen University, Aachen, Germany
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49
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Cherry AA, Ananvoranich S. Characterization of a homolog of DEAD-box RNA helicases in Toxoplasma gondii as a marker of cytoplasmic mRNP stress granules. Gene 2014; 543:34-44. [PMID: 24709106 DOI: 10.1016/j.gene.2014.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/23/2014] [Accepted: 04/03/2014] [Indexed: 11/27/2022]
Abstract
Toxoplasma gondii is an obligate intracellular protozoan which infects one-third of the human population. Due to its high infection prevalence, Toxoplasma offers an ideal system for the study of host-parasite interaction. Similar to other eukaryotes, Toxoplasma maintains levels and localization of cytoplasmic mRNAs throughout its life cycle as part of a gene regulation network to meet all cellular and biochemical requirements. More recently, it was reported that the presence of cytoplasmic mRNA granules could contribute to the parasite pathogenesis and viability. Here we identified a novel Toxoplasma DEAD-box RNA helicase, referred to as Toxoplasma gondiiHomolog of DOZI (TgHoDI), because of its high homology (81%) to Plasmodium DOZI. TgHoDI is the functional ortholog of yeast DHH1, and its function was authenticated by complementation studies in Δdhh1 yeast strain. We demonstrated that TgHoDI is a marker of cytoplasmic RNA stress granules, which assemble when the parasites experience cellular stresses and translational arrest.
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Affiliation(s)
- Ahmed Adnan Cherry
- The Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B3P4, Canada
| | - Sirinart Ananvoranich
- The Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B3P4, Canada.
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Kinkhabwala A, Khmelinskii A, Knop M. Analytical model for macromolecular partitioning during yeast cell division. BMC BIOPHYSICS 2014; 7:10. [PMID: 25737777 PMCID: PMC4347614 DOI: 10.1186/s13628-014-0010-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 08/29/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partitioning of the macromolecular content of the parent cell - which includes proteins, DNA, RNA, large proteinaceous assemblies and organelles - can be achieved by both passive (e.g. diffusion, localized retention sites) and active (e.g. motor-driven transport) processes operating in the presence of external polarity cues, internal asymmetries, spontaneous symmetry breaking, or stochastic effects. However, the quantitative contribution of different processes to the partitioning of macromolecular content is difficult to evaluate. RESULTS Here we developed an analytical model that allows rapid quantitative assessment of partitioning as a function of various parameters in the budding yeast Saccharomyces cerevisiae. This model exposes quantitative degeneracies among the physical parameters that govern macromolecular partitioning, and reveals regions of the solution space where diffusion is sufficient to drive asymmetric partitioning and regions where asymmetric partitioning can only be achieved through additional processes such as motor-driven transport. Application of the model to different macromolecular assemblies suggests that partitioning of protein aggregates and episomes, but not prions, is diffusion-limited in yeast, consistent with previous reports. CONCLUSIONS In contrast to computationally intensive stochastic simulations of particular scenarios, our analytical model provides an efficient and comprehensive overview of partitioning as a function of global and macromolecule-specific parameters. Identification of quantitative degeneracies among these parameters highlights the importance of their careful measurement for a given macromolecular species in order to understand the dominant processes responsible for its observed partitioning.
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Affiliation(s)
- Ali Kinkhabwala
- Abteilung Systemische Zellbiologie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, Dortmund 44227, Germany
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) and Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH-Allianz, Im Neuenheimer Feld 282, Heidelberg 69120, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) and Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH-Allianz, Im Neuenheimer Feld 282, Heidelberg 69120, Germany
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